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: ENST00000371761
Querying Taster for transcript #2: ENST00000396148
Querying Taster for transcript #3: ENST00000262662
MT speed 0.04 s - this script 2.407873 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000371761(MANE Select)	CDKN2C	Benign	1\|199	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000396148	CDKN2C	Benign	1\|199	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000262662	CDKN2C	Benign	1\|199	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD

MutationT@ster 2025

Variant:

1:50971575A>G_1_ENST00000371761

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 1|199 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr1:50971575A>G (GRCh38)

Gene symbol

CDKN2C

Gene constraints

LOEUF: 0.94, LOF (oe): 0.45, misssense (oe): 0.72, synonymous (oe): 0.85 ? (gnomAD)

Ensembl transcript ID

ENST00000371761.4

Genbank transcript ID

NM_078626 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.129+1078A>G
g.10831A>G

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	rs3176459
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	7496	31743	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.077	0
	0.908	0.002
(flanking)	0.363	0.003

?

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

1

Strand

1

Original gDNA sequence snippet

TTTATCTTGTTATTGCTGCTACATTAAGTAATGATTTTTTT

Altered gDNA sequence snippet

TTTATCTTGTTATTGCTGCTGCATTAAGTAATGATTTTTTT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAEPWGNELA SAAARGDLEQ LTSLLQNNVN VNAQNGFGRT ALQVMKLGNP EIARRLLLRG
ANPDLKDRTG FAVIHDAARA GFLDTLQTLL EFQADVNIED NEGNLPLHLA AKEGHLRVVE
FLVKHTASNV GHRNHKGDTA CDLARLYGRN EVVSLMQANG AGGATNLQ*

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

125 / 125

Last intron/exon boundary

253

Theoretical NMD boundary in CDS

78

Length of CDS

507

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

10831

Chromosomal position

50971575

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

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MutationT@ster 2025

Variant:

1:50971575A>G_2_ENST00000396148

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 1|199 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr1:50971575A>G (GRCh38)

Gene symbol

CDKN2C

Gene constraints

LOEUF: 0.94, LOF (oe): 0.45, misssense (oe): 0.72, synonymous (oe): 0.85 ? (gnomAD)

Ensembl transcript ID

ENST00000396148.2

Genbank transcript ID

NM_001262 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.129+1078A>G
g.10831A>G

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	rs3176459
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	7496	31743	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.077	0
	0.908	0.002
(flanking)	0.363	0.003

?

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

1

Strand

1

Original gDNA sequence snippet

TTTATCTTGTTATTGCTGCTACATTAAGTAATGATTTTTTT

Altered gDNA sequence snippet

TTTATCTTGTTATTGCTGCTGCATTAAGTAATGATTTTTTT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAEPWGNELA SAAARGDLEQ LTSLLQNNVN VNAQNGFGRT ALQVMKLGNP EIARRLLLRG
ANPDLKDRTG FAVIHDAARA GFLDTLQTLL EFQADVNIED NEGNLPLHLA AKEGHLRVVE
FLVKHTASNV GHRNHKGDTA CDLARLYGRN EVVSLMQANG AGGATNLQ*

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

1206 / 1206

Last intron/exon boundary

1334

Theoretical NMD boundary in CDS

78

Length of CDS

507

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

10831

Chromosomal position

50971575

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:

1:50971575A>G_3_ENST00000262662

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 1|199 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr1:50971575A>G (GRCh38)

Gene symbol

CDKN2C

Gene constraints

LOEUF: 0.94, LOF (oe): 0.45, misssense (oe): 0.72, synonymous (oe): 0.85 ? (gnomAD)

Ensembl transcript ID

ENST00000262662.5

Genbank transcript ID

NM_001429675 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.129+1078A>G
g.10831A>G

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	rs3176459
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	7496	31743	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.077	0
	0.908	0.002
(flanking)	0.363	0.003

?

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

1

Strand

1

Original gDNA sequence snippet

TTTATCTTGTTATTGCTGCTACATTAAGTAATGATTTTTTT

Altered gDNA sequence snippet

TTTATCTTGTTATTGCTGCTGCATTAAGTAATGATTTTTTT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAEPWGNELA SAAARGDLEQ LTSLLQNNVN VNAQNGFGRT ALQVMKLGNP EIARRLLLRG
ANPDLKDRTG FAVIHDAARA GFLDTLQTLL EFQADVNIED NEGNLPLHLA AKEGHLRVVE
FLVKHTASNV GHRNHKGDTA CDLARLYGRN EVVSLMQANG AGGATNLQ*

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

2035 / 2035

Last intron/exon boundary

2163

Theoretical NMD boundary in CDS

78

Length of CDS

507

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

10831

Chromosomal position

50971575

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