MutationT@ster 2025

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Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000254976
Querying Taster for transcript #2: ENST00000691665
Querying Taster for transcript #3: ENST00000304886
Querying Taster for transcript #4: ENST00000685131
Querying Taster for transcript #5: ENST00000687785
Querying Taster for transcript #6: ENST00000706269
Querying Taster for transcript #7: ENST00000691353
Querying Taster for transcript #8: ENST00000691161
Querying Taster for transcript #9: ENST00000692411
Querying Taster for transcript #10: ENST00000690812
Querying Taster for transcript #11: ENST00000693325
Querying Taster for transcript #12: ENST00000689858
Querying Taster for transcript #13: ENST00000689757
MT speed 0.19 s - this script 2.6522 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000254976(MANE Select)	SNAP25	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000691665	SNAP25	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000304886	SNAP25	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000685131	SNAP25	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000687785	SNAP25	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000706269	SNAP25	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000691353	SNAP25	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000691161	SNAP25	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000692411	SNAP25	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000690812	SNAP25	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000693325	SNAP25	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000689858	SNAP25	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000689757	SNAP25	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD

MutationT@ster 2025

Variant:

20:10262538G>A_1_ENST00000254976

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr20:10262538G>A (GRCh38)

Gene symbol

SNAP25

Gene constraints

LOEUF: 0.29, LOF (oe): 0.09, misssense (oe): 0.44, synonymous (oe): 0.62 ? (gnomAD)

Ensembl transcript ID

ENST00000254976.7

Genbank transcript ID

NM_130811 (exact from MANE), NM_001424416 (by similarity), NM_001322906 (by similarity), NM_001322909 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-63-12891G>A
g.90144G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs362562
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	10738	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.622	0.002
	0.138	0.002
(flanking)	1.299	0.004

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

20

Strand

1

Original gDNA sequence snippet

CCTCTTTTCCTGATTCAGTGGTTTGTTGATTCCTCTAAGTA

Altered gDNA sequence snippet

CCTCTTTTCCTGATTCAGTGATTTGTTGATTCCTCTAAGTA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAEDADMRNE LEEMQRRADQ LADESLESTR RMLQLVEESK DAGIRTLVML DEQGEQLERI
EEGMDQINKD MKEAEKNLTD LGKFCGLCVC PCNKLKSSDA YKKAWGNNQD GVVASQPARV
VDEREQMAIS GGFIRRVTND ARENEMDENL EQVSGIIGNL RHMALDMGNE IDTQNRQIDR
IMEKADSNKT RIDEANQRAT KMLGSG*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

212 / 212

Last intron/exon boundary

763

Theoretical NMD boundary in CDS

501

Length of CDS

621

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

90144

Chromosomal position

10262538

Speed

0.02 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

20:10262538G>A_2_ENST00000691665

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr20:10262538G>A (GRCh38)

Gene symbol

SNAP25

Gene constraints

LOEUF: 0.29, LOF (oe): 0.09, misssense (oe): 0.44, synonymous (oe): 0.62 ? (gnomAD)

Ensembl transcript ID

ENST00000691665.1

Genbank transcript ID

NM_001322903 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-63-12891G>A
g.90144G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs362562
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	10738	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.622	0.002
	0.138	0.002
(flanking)	1.299	0.004

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

20

Strand

1

Original gDNA sequence snippet

CCTCTTTTCCTGATTCAGTGGTTTGTTGATTCCTCTAAGTA

Altered gDNA sequence snippet

CCTCTTTTCCTGATTCAGTGATTTGTTGATTCCTCTAAGTA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAEDADMRNE LEEMQRRADQ LADESLESTR RMLQLVEESK DAGIRTLVML DEQGEQLERI
EEGMDQINKD MKEAEKNLTD LGKFCGLCVC PCNKLKSSDA YKKAWGNNQD GVVASQPARV
VDEREQMAIS GGFIRRVTND ARENEMDENL EQVSGIIGNL RHMALDMGNE IDTQNRQIDR
IMEKADSNKT RIDEANQRAT KMLGSG*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

339 / 339

Last intron/exon boundary

890

Theoretical NMD boundary in CDS

501

Length of CDS

621

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

90144

Chromosomal position

10262538

Speed

0.01 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

20:10262538G>A_3_ENST00000304886

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr20:10262538G>A (GRCh38)

Gene symbol

SNAP25

Gene constraints

LOEUF: 0.32, LOF (oe): 0.10, misssense (oe): 0.48, synonymous (oe): 0.78 ? (gnomAD)

Ensembl transcript ID

ENST00000304886.6

Genbank transcript ID

NM_001424415 (by similarity), NM_003081 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-63-12891G>A
g.90144G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs362562
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	10738	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.622	0.002
	0.138	0.002
(flanking)	1.299	0.004

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

20

Strand

1

Original gDNA sequence snippet

CCTCTTTTCCTGATTCAGTGGTTTGTTGATTCCTCTAAGTA

Altered gDNA sequence snippet

CCTCTTTTCCTGATTCAGTGATTTGTTGATTCCTCTAAGTA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAEDADMRNE LEEMQRRADQ LADESLESTR RMLQLVEESK DAGIRTLVML DEQGEQLDRV
EEGMNHINQD MKEAEKNLKD LGKCCGLFIC PCNKLKSSDA YKKAWGNNQD GVVASQPARV
VDEREQMAIS GGFIRRVTND ARENEMDENL EQVSGIIGNL RHMALDMGNE IDTQNRQIDR
IMEKADSNKT RIDEANQRAT KMLGSG*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

209 / 209

Last intron/exon boundary

760

Theoretical NMD boundary in CDS

501

Length of CDS

621

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

90144

Chromosomal position

10262538

Speed

0.01 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

20:10262538G>A_4_ENST00000685131

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr20:10262538G>A (GRCh38)

Gene symbol

SNAP25

Gene constraints

LOEUF: 0.29, LOF (oe): 0.09, misssense (oe): 0.44, synonymous (oe): 0.62 ? (gnomAD)

Ensembl transcript ID

ENST00000685131.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-63-12891G>A
g.90144G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs362562
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	10738	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.622	0.002
	0.138	0.002
(flanking)	1.299	0.004

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

20

Strand

1

Original gDNA sequence snippet

CCTCTTTTCCTGATTCAGTGGTTTGTTGATTCCTCTAAGTA

Altered gDNA sequence snippet

CCTCTTTTCCTGATTCAGTGATTTGTTGATTCCTCTAAGTA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAEDADMRNE LEEMQRRADQ LADESLESTR RMLQLVEESK DAGIRTLVML DEQGEQLERI
EEGMDQINKD MKEAEKNLTD LGKFCGLCVC PCNKLKSSDA YKKAWGNNQD GVVASQPARV
VDEREQMAIS GGFIRRVTND ARENEMDENL EQVSGIIGNL RHMALDMGNE IDTQNRQIDR
IMEKADSNKT RIDEANQRAT KMLGSG*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

181 / 181

Last intron/exon boundary

732

Theoretical NMD boundary in CDS

501

Length of CDS

621

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

90144

Chromosomal position

10262538

Speed

0.02 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

20:10262538G>A_5_ENST00000687785

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr20:10262538G>A (GRCh38)

Gene symbol

SNAP25

Gene constraints

LOEUF: 0.29, LOF (oe): 0.09, misssense (oe): 0.44, synonymous (oe): 0.62 ? (gnomAD)

Ensembl transcript ID

ENST00000687785.1

Genbank transcript ID

NM_001322908 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-63-12891G>A
g.90144G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs362562
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	10738	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.622	0.002
	0.138	0.002
(flanking)	1.299	0.004

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

20

Strand

1

Original gDNA sequence snippet

CCTCTTTTCCTGATTCAGTGGTTTGTTGATTCCTCTAAGTA

Altered gDNA sequence snippet

CCTCTTTTCCTGATTCAGTGATTTGTTGATTCCTCTAAGTA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAEDADMRNE LEEMQRRADQ LADESLESTR RMLQLVEESK DAGIRTLVML DEQGEQLERI
EEGMDQINKD MKEAEKNLTD LGKFCGLCVC PCNKLKSSDA YKKAWGNNQD GVVASQPARV
VDEREQMAIS GGFIRRVTND ARENEMDENL EQVSGIIGNL RHMALDMGNE IDTQNRQIDR
IMEKADSNKT RIDEANQRAT KMLGSG*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

335 / 335

Last intron/exon boundary

886

Theoretical NMD boundary in CDS

501

Length of CDS

621

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

90144

Chromosomal position

10262538

Speed

0.01 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

20:10262538G>A_6_ENST00000706269

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr20:10262538G>A (GRCh38)

Gene symbol

SNAP25

Gene constraints

no data

Ensembl transcript ID

ENST00000706269.1

Genbank transcript ID

NM_001322902 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-63-12891G>A
g.90144G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs362562
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	10738	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.622	0.002
	0.138	0.002
(flanking)	1.299	0.004

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

20

Strand

1

Original gDNA sequence snippet

CCTCTTTTCCTGATTCAGTGGTTTGTTGATTCCTCTAAGTA

Altered gDNA sequence snippet

CCTCTTTTCCTGATTCAGTGATTTGTTGATTCCTCTAAGTA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAEDADMRNE LEEMQRRADQ LADESLESTR RMLQLVEESK DAGIRTLVML DEQGEQLDRV
EEGMNHINQD MKEAEKNLKD LGKCCGLFIC PCNKLKSSDA YKKAWGNNQD GVVASQPARV
VDEREQMAIS GGFIRRVTND ARENEMDENL EQVSGIIGNL RHMALDMGNE IDTQNRQIDR
IMEKADSNKT RIDEANQRAT KMLGSG*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

119 / 119

Last intron/exon boundary

670

Theoretical NMD boundary in CDS

501

Length of CDS

621

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

90144

Chromosomal position

10262538

Speed

0.02 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

20:10262538G>A_7_ENST00000691353

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr20:10262538G>A (GRCh38)

Gene symbol

SNAP25

Gene constraints

LOEUF: 0.29, LOF (oe): 0.09, misssense (oe): 0.44, synonymous (oe): 0.62 ? (gnomAD)

Ensembl transcript ID

ENST00000691353.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-262-2941G>A
g.90144G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs362562
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	10738	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.622	0.002
	0.138	0.002
(flanking)	1.299	0.004

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

20

Strand

1

Original gDNA sequence snippet

CCTCTTTTCCTGATTCAGTGGTTTGTTGATTCCTCTAAGTA

Altered gDNA sequence snippet

CCTCTTTTCCTGATTCAGTGATTTGTTGATTCCTCTAAGTA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAEDADMRNE LEEMQRRADQ LADESLESTR RMLQLVEESK DAGIRTLVML DEQGEQLERI
EEGMDQINKD MKEAEKNLTD LGKFCGLCVC PCNKLKSSDA YKKAWGNNQD GVVASQPARV
VDEREQMAIS GGFIRRVTND ARENEMDENL EQVSGIIGNL RHMALDMGNE IDTQNRQIDR
IMEKADSNKT RIDEANQRAT KMLGSG*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

318 / 318

Last intron/exon boundary

869

Theoretical NMD boundary in CDS

501

Length of CDS

621

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

90144

Chromosomal position

10262538

Speed

0.02 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

20:10262538G>A_8_ENST00000691161

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr20:10262538G>A (GRCh38)

Gene symbol

SNAP25

Gene constraints

LOEUF: 0.29, LOF (oe): 0.09, misssense (oe): 0.44, synonymous (oe): 0.62 ? (gnomAD)

Ensembl transcript ID

ENST00000691161.1

Genbank transcript ID

NM_001322907 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-63-12891G>A
g.90144G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs362562
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	10738	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.622	0.002
	0.138	0.002
(flanking)	1.299	0.004

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

20

Strand

1

Original gDNA sequence snippet

CCTCTTTTCCTGATTCAGTGGTTTGTTGATTCCTCTAAGTA

Altered gDNA sequence snippet

CCTCTTTTCCTGATTCAGTGATTTGTTGATTCCTCTAAGTA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAEDADMRNE LEEMQRRADQ LADESLESTR RMLQLVEESK DAGIRTLVML DEQGEQLERI
EEGMDQINKD MKEAEKNLTD LGKFCGLCVC PCNKLKSSDA YKKAWGNNQD GVVASQPARV
VDEREQMAIS GGFIRRVTND ARENEMDENL EQVSGIIGNL RHMALDMGNE IDTQNRQIDR
IMEKADSNKT RIDEANQRAT KMLGSG*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

387 / 387

Last intron/exon boundary

938

Theoretical NMD boundary in CDS

501

Length of CDS

621

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

90144

Chromosomal position

10262538

Speed

0.01 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

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MutationT@ster 2025

Variant:

20:10262538G>A_9_ENST00000692411

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr20:10262538G>A (GRCh38)

Gene symbol

SNAP25

Gene constraints

LOEUF: 0.29, LOF (oe): 0.09, misssense (oe): 0.44, synonymous (oe): 0.62 ? (gnomAD)

Ensembl transcript ID

ENST00000692411.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-64+1223G>A
g.90144G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs362562
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	10738	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.622	0.002
	0.138	0.002
(flanking)	1.299	0.004

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

20

Strand

1

Original gDNA sequence snippet

CCTCTTTTCCTGATTCAGTGGTTTGTTGATTCCTCTAAGTA

Altered gDNA sequence snippet

CCTCTTTTCCTGATTCAGTGATTTGTTGATTCCTCTAAGTA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAEDADMRNE LEEMQRRADQ LADESLESTR RMLQLVEESK DAGIRTLVML DEQGEQLERI
EEGMDQINKD MKEAEKNLTD LGKFCGLCVC PCNKLKSSDA YKKAWGNNQD GVVASQPARV
VDEREQMAIS GGFIRRVTND ARENEMDENL EQVSGIIGNL RHMALDMGNE IDTQNRQIDR
IMEKADSNKT RIDEANQRAT KMLGSG*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

201 / 201

Last intron/exon boundary

752

Theoretical NMD boundary in CDS

501

Length of CDS

621

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

90144

Chromosomal position

10262538

Speed

0.01 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

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MutationT@ster 2025

Variant:

20:10262538G>A_10_ENST00000690812

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr20:10262538G>A (GRCh38)

Gene symbol

SNAP25

Gene constraints

LOEUF: 0.29, LOF (oe): 0.09, misssense (oe): 0.44, synonymous (oe): 0.62 ? (gnomAD)

Ensembl transcript ID

ENST00000690812.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-64+3137G>A
g.90144G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs362562
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	10738	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.622	0.002
	0.138	0.002
(flanking)	1.299	0.004

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

20

Strand

1

Original gDNA sequence snippet

CCTCTTTTCCTGATTCAGTGGTTTGTTGATTCCTCTAAGTA

Altered gDNA sequence snippet

CCTCTTTTCCTGATTCAGTGATTTGTTGATTCCTCTAAGTA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAEDADMRNE LEEMQRRADQ LADESLESTR RMLQLVEESK DAGIRTLVML DEQGEQLERI
EEGMDQINKD MKEAEKNLTD LGKFCGLCVC PCNKLKSSDA YKKAWGNNQD GVVASQPARV
VDEREQMAIS GGFIRRVTND ARENEMDENL EQVSGIIGNL RHMALDMGNE IDTQNRQIDR
IMEKADSNKT RIDEANQRAT KMLGSG*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

219 / 219

Last intron/exon boundary

770

Theoretical NMD boundary in CDS

501

Length of CDS

621

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

90144

Chromosomal position

10262538

Speed

0.02 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

20:10262538G>A_11_ENST00000693325

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr20:10262538G>A (GRCh38)

Gene symbol

SNAP25

Gene constraints

LOEUF: 0.29, LOF (oe): 0.09, misssense (oe): 0.44, synonymous (oe): 0.62 ? (gnomAD)

Ensembl transcript ID

ENST00000693325.1

Genbank transcript ID

NM_001322910 (by similarity), NM_001322904 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-63-12891G>A
g.90144G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs362562
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	10738	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.622	0.002
	0.138	0.002
(flanking)	1.299	0.004

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

20

Strand

1

Original gDNA sequence snippet

CCTCTTTTCCTGATTCAGTGGTTTGTTGATTCCTCTAAGTA

Altered gDNA sequence snippet

CCTCTTTTCCTGATTCAGTGATTTGTTGATTCCTCTAAGTA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAEDADMRNE LEEMQRRADQ LADESLESTR RMLQLVEESK DAGIRTLVML DEQGEQLERI
EEGMDQINKD MKEAEKNLTD LGKFCGLCVC PCNKLKSSDA YKKAWGNNQD GVVASQPARV
VDEREQMAIS GGFIRRVTND ARENEMDENL EQVSGIIGNL RHMALDMGNE IDTQNRQIDR
IMEKADSNKT RIDEANQRAT KMLGSG*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

282 / 282

Last intron/exon boundary

833

Theoretical NMD boundary in CDS

501

Length of CDS

621

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

90144

Chromosomal position

10262538

Speed

0.01 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

20:10262538G>A_12_ENST00000689858

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr20:10262538G>A (GRCh38)

Gene symbol

SNAP25

Gene constraints

LOEUF: 0.29, LOF (oe): 0.09, misssense (oe): 0.44, synonymous (oe): 0.62 ? (gnomAD)

Ensembl transcript ID

ENST00000689858.1

Genbank transcript ID

NM_001322905 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-63-12891G>A
g.90144G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs362562
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	10738	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.622	0.002
	0.138	0.002
(flanking)	1.299	0.004

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

20

Strand

1

Original gDNA sequence snippet

CCTCTTTTCCTGATTCAGTGGTTTGTTGATTCCTCTAAGTA

Altered gDNA sequence snippet

CCTCTTTTCCTGATTCAGTGATTTGTTGATTCCTCTAAGTA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAEDADMRNE LEEMQRRADQ LADESLESTR RMLQLVEESK DAGIRTLVML DEQGEQLERI
EEGMDQINKD MKEAEKNLTD LGKFCGLCVC PCNKLKSSDA YKKAWGNNQD GVVASQPARV
VDEREQMAIS GGFIRRVTND ARENEMDENL EQVSGIIGNL RHMALDMGNE IDTQNRQIDR
IMEKADSNKT RIDEANQRAT KMLGSG*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

235 / 235

Last intron/exon boundary

786

Theoretical NMD boundary in CDS

501

Length of CDS

621

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

90144

Chromosomal position

10262538

Speed

0.02 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

20:10262538G>A_13_ENST00000689757

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr20:10262538G>A (GRCh38)

Gene symbol

SNAP25

Gene constraints

LOEUF: 0.29, LOF (oe): 0.09, misssense (oe): 0.44, synonymous (oe): 0.62 ? (gnomAD)

Ensembl transcript ID

ENST00000689757.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-64+3137G>A
g.90144G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs362562
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	10738	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.622	0.002
	0.138	0.002
(flanking)	1.299	0.004

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

20

Strand

1

Original gDNA sequence snippet

CCTCTTTTCCTGATTCAGTGGTTTGTTGATTCCTCTAAGTA

Altered gDNA sequence snippet

CCTCTTTTCCTGATTCAGTGATTTGTTGATTCCTCTAAGTA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAEDADMRNE LEEMQRRADQ LADESLESTR RMLQLVEESK DAGIRTLVML DEQGEQLERI
EEGMDQINKD MKEAEKNLTD LGKFCGLCVC PCNKLKSSDA YKKAWGNNQD GVVASQPARV
VDEREQMAIS GGFIRRVTND ARENEMDENL EQVSGIIGNL RHMALDMGNE IDTQNRQIDR
IMEKADSNKT RIDEANQRAT KMLGSG*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

310 / 310

Last intron/exon boundary

861

Theoretical NMD boundary in CDS

501

Length of CDS

621

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

90144

Chromosomal position

10262538

Speed

0.01 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table