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: ENST00000676153
Querying Taster for transcript #2: ENST00000675184
Querying Taster for transcript #3: ENST00000615928
Querying Taster for transcript #4: ENST00000676433
Querying Taster for transcript #5: ENST00000255380
MT speed 0.13 s - this script 2.560035 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
ENST00000676153(MANE Select)	CHRM3	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000675184	CHRM3	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000615928	CHRM3	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000676433	CHRM3	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000255380	CHRM3	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD

MutationT@ster 2025

Variant:

1:239888040G>A_1_ENST00000676153

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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

Chr1:239888040G>A (GRCh38)

Gene symbol

CHRM3

Gene constraints

LOEUF: 0.42, LOF (oe): 0.25, misssense (oe): 0.74, synonymous (oe): 0.95 ? (gnomAD)

Ensembl transcript ID

ENST00000676153.1

Genbank transcript ID

NM_001375978 (exact from MANE), NM_001375982 (by similarity), NM_001347716 (by similarity), NM_001375983 (by similarity), NM_001375979 (by similarity), NM_001375984 (by similarity), NM_001375981 (by similarity), NM_001375985 (by similarity), NM_001375980 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-19-19393G>A
g.501476G>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	rs10495447
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	5275	27710	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.288	0
	-0.457	0
(flanking)	-0.329	0

?

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

GTTTAAGTCGTGGTCTTGATGGTTATTGTGGTGTTTATCTC

Altered gDNA sequence snippet

GTTTAAGTCGTGGTCTTGATAGTTATTGTGGTGTTTATCTC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MTLHNNSTTS PLFPNISSSW IHSPSDAGLP PGTVTHFGSY NVSRAAGNFS SPDGTTDDPL
GGHTVWQVVF IAFLTGILAL VTIIGNILVI VSFKVNKQLK TVNNYFLLSL ACADLIIGVI
SMNLFTTYII MNRWALGNLA CDLWLAIDYV ASNASVMNLL VISFDRYFSI TRPLTYRAKR
TTKRAGVMIG LAWVISFVLW APAILFWQYF VGKRTVPPGE CFIQFLSEPT ITFGTAIAAF
YMPVTIMTIL YWRIYKETEK RTKELAGLQA SGTEAETENF VHPTGSSRSC SSYELQQQSM
KRSNRRKYGR CHFWFTTKSW KPSSEQMDQD HSSSDSWNNN DAAASLENSA SSDEEDIGSE
TRAIYSIVLK LPGHSTILNS TKLPSSDNLQ VPEEELGMVD LERKADKLQA QKSVDDGGSF
PKSFSKLPIQ LESAVDTAKT SDVNSSVGKS TATLPLSFKE ATLAKRFALK TRSQITKRKR
MSLVKEKKAA QTLSAILLAF IITWTPYNIM VLVNTFCDSC IPKTFWNLGY WLCYINSTVN
PVCYALCNKT FRTTFKMLLL CQCDKKKRRK QQYQQRQSVI FHKRAPEQAL *

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

1181 / 1181

Last intron/exon boundary

1161

Theoretical NMD boundary in CDS

cannot be calculated, distance between start ATG and last intron/exon boundary is too small

Length of CDS

1773

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

501476

Chromosomal position

239888040

Speed

0.05 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:

1:239888040G>A_2_ENST00000675184

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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

Chr1:239888040G>A (GRCh38)

Gene symbol

CHRM3

Gene constraints

LOEUF: 0.42, LOF (oe): 0.25, misssense (oe): 0.74, synonymous (oe): 0.95 ? (gnomAD)

Ensembl transcript ID

ENST00000675184.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-19-19393G>A
g.501476G>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	rs10495447
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	5275	27710	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.288	0
	-0.457	0
(flanking)	-0.329	0

?

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

GTTTAAGTCGTGGTCTTGATGGTTATTGTGGTGTTTATCTC

Altered gDNA sequence snippet

GTTTAAGTCGTGGTCTTGATAGTTATTGTGGTGTTTATCTC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MTLHNNSTTS PLFPNISSSW IHSPSDAGLP PGTVTHFGSY NVSRAAGNFS SPDGTTDDPL
GGHTVWQVVF IAFLTGILAL VTIIGNILVI VSFKVNKQLK TVNNYFLLSL ACADLIIGVI
SMNLFTTYII MNRWALGNLA CDLWLAIDYV ASNASVMNLL VISFDRYFSI TRPLTYRAKR
TTKRAGVMIG LAWVISFVLW APAILFWQYF VGKRTVPPGE CFIQFLSEPT ITFGTAIAAF
YMPVTIMTIL YWRIYKETEK RTKELAGLQA SGTEAETENF VHPTGSSRSC SSYELQQQSM
KRSNRRKYGR CHFWFTTKSW KPSSEQMDQD HSSSDSWNNN DAAASLENSA SSDEEDIGSE
TRAIYSIVLK LPGHSTILNS TKLPSSDNLQ VPEEELGMVD LERKADKLQA QKSVDDGGSF
PKSFSKLPIQ LESAVDTAKT SDVNSSVGKS TATLPLSFKE ATLAKRFALK TRSQITKRKR
MSLVKEKKAA QTLSAILLAF IITWTPYNIM VLVNTFCDSC IPKTFWNLGY WLCYINSTVN
PVCYALCNKT FRTTFKMLLL CQCDKKKRRK QQYQQRQSVI FHKRAPEQAL *

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

796 / 796

Last intron/exon boundary

776

Theoretical NMD boundary in CDS

cannot be calculated, distance between start ATG and last intron/exon boundary is too small

Length of CDS

1773

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

501476

Chromosomal position

239888040

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:

1:239888040G>A_3_ENST00000615928

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

Chr1:239888040G>A (GRCh38)

Gene symbol

CHRM3

Gene constraints

LOEUF: 0.42, LOF (oe): 0.25, misssense (oe): 0.74, synonymous (oe): 0.95 ? (gnomAD)

Ensembl transcript ID

ENST00000615928.5

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-19-19393G>A
g.501476G>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	rs10495447
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	5275	27710	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.288	0
	-0.457	0
(flanking)	-0.329	0

?

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

GTTTAAGTCGTGGTCTTGATGGTTATTGTGGTGTTTATCTC

Altered gDNA sequence snippet

GTTTAAGTCGTGGTCTTGATAGTTATTGTGGTGTTTATCTC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MTLHNNSTTS PLFPNISSSW IHSPSDAGLP PGTVTHFGSY NVSRAAGNFS SPDGTTDDPL
GGHTVWQVVF IAFLTGILAL VTIIGNILVI VSFKVNKQLK TVNNYFLLSL ACADLIIGVI
SMNLFTTYII MNRWALGNLA CDLWLAIDYV ASNASVMNLL VISFDRYFSI TRPLTYRAKR
TTKRAGVMIG LAWVISFVLW APAILFWQYF VGKRTVPPGE CFIQFLSEPT ITFGTAIAAF
YMPVTIMTIL YWRIYKETEK RTKELAGLQA SGTEAETENF VHPTGSSRSC SSYELQQQSM
KRSNRRKYGR CHFWFTTKSW KPSSEQMDQD HSSSDSWNNN DAAASLENSA SSDEEDIGSE
TRAIYSIVLK LPGHSTILNS TKLPSSDNLQ VPEEELGMVD LERKADKLQA QKSVDDGGSF
PKSFSKLPIQ LESAVDTAKT SDVNSSVGKS TATLPLSFKE ATLAKRFALK TRSQITKRKR
MSLVKEKKAA QTLSAILLAF IITWTPYNIM VLVNTFCDSC IPKTFWNLGY WLCYINSTVN
PVCYALCNKT FRTTFKMLLL CQCDKKKRRK QQYQQRQSVI FHKRAPEQAL *

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

504 / 504

Last intron/exon boundary

484

Theoretical NMD boundary in CDS

cannot be calculated, distance between start ATG and last intron/exon boundary is too small

Length of CDS

1773

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

501476

Chromosomal position

239888040

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:

1:239888040G>A_4_ENST00000676433

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

Chr1:239888040G>A (GRCh38)

Gene symbol

CHRM3

Gene constraints

LOEUF: 0.42, LOF (oe): 0.25, misssense (oe): 0.74, synonymous (oe): 0.95 ? (gnomAD)

Ensembl transcript ID

ENST00000676433.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-19-19393G>A
g.501476G>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	rs10495447
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	5275	27710	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.288	0
	-0.457	0
(flanking)	-0.329	0

?

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

GTTTAAGTCGTGGTCTTGATGGTTATTGTGGTGTTTATCTC

Altered gDNA sequence snippet

GTTTAAGTCGTGGTCTTGATAGTTATTGTGGTGTTTATCTC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MTLHNNSTTS PLFPNISSSW IHSPSDAGLP PGTVTHFGSY NVSRAAGNFS SPDGTTDDPL
GGHTVWQVVF IAFLTGILAL VTIIGNILVI VSFKVNKQLK TVNNYFLLSL ACADLIIGVI
SMNLFTTYII MNRWALGNLA CDLWLAIDYV ASNASVMNLL VISFDRYFSI TRPLTYRAKR
TTKRAGVMIG LAWVISFVLW APAILFWQYF VGKRTVPPGE CFIQFLSEPT ITFGTAIAAF
YMPVTIMTIL YWRIYKETEK RTKELAGLQA SGTEAETENF VHPTGSSRSC SSYELQQQSM
KRSNRRKYGR CHFWFTTKSW KPSSEQMDQD HSSSDSWNNN DAAASLENSA SSDEEDIGSE
TRAIYSIVLK LPGHSTILNS TKLPSSDNLQ VPEEELGMVD LERKADKLQA QKSVDDGGSF
PKSFSKLPIQ LESAVDTAKT SDVNSSVGKS TATLPLSFKE ATLAKRFALK TRSQITKRKR
MSLVKEKKAA QTLSAILLAF IITWTPYNIM VLVNTFCDSC IPKTFWNLGY WLCYINSTVN
PVCYALCNKT FRTTFKMLLL CQCDKKKRRK QQYQQRQSVI FHKRAPEQAL *

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

604 / 604

Last intron/exon boundary

584

Theoretical NMD boundary in CDS

cannot be calculated, distance between start ATG and last intron/exon boundary is too small

Length of CDS

1773

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

501476

Chromosomal position

239888040

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:

1:239888040G>A_5_ENST00000255380

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

Chr1:239888040G>A (GRCh38)

Gene symbol

CHRM3

Gene constraints

LOEUF: 0.42, LOF (oe): 0.25, misssense (oe): 0.74, synonymous (oe): 0.95 ? (gnomAD)

Ensembl transcript ID

ENST00000255380.8

Genbank transcript ID

NM_000740 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-19-19393G>A
g.501476G>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	rs10495447
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	5275	27710	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.288	0
	-0.457	0
(flanking)	-0.329	0

?

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

GTTTAAGTCGTGGTCTTGATGGTTATTGTGGTGTTTATCTC

Altered gDNA sequence snippet

GTTTAAGTCGTGGTCTTGATAGTTATTGTGGTGTTTATCTC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MTLHNNSTTS PLFPNISSSW IHSPSDAGLP PGTVTHFGSY NVSRAAGNFS SPDGTTDDPL
GGHTVWQVVF IAFLTGILAL VTIIGNILVI VSFKVNKQLK TVNNYFLLSL ACADLIIGVI
SMNLFTTYII MNRWALGNLA CDLWLAIDYV ASNASVMNLL VISFDRYFSI TRPLTYRAKR
TTKRAGVMIG LAWVISFVLW APAILFWQYF VGKRTVPPGE CFIQFLSEPT ITFGTAIAAF
YMPVTIMTIL YWRIYKETEK RTKELAGLQA SGTEAETENF VHPTGSSRSC SSYELQQQSM
KRSNRRKYGR CHFWFTTKSW KPSSEQMDQD HSSSDSWNNN DAAASLENSA SSDEEDIGSE
TRAIYSIVLK LPGHSTILNS TKLPSSDNLQ VPEEELGMVD LERKADKLQA QKSVDDGGSF
PKSFSKLPIQ LESAVDTAKT SDVNSSVGKS TATLPLSFKE ATLAKRFALK TRSQITKRKR
MSLVKEKKAA QTLSAILLAF IITWTPYNIM VLVNTFCDSC IPKTFWNLGY WLCYINSTVN
PVCYALCNKT FRTTFKMLLL CQCDKKKRRK QQYQQRQSVI FHKRAPEQAL *

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

780 / 780

Last intron/exon boundary

760

Theoretical NMD boundary in CDS

cannot be calculated, distance between start ATG and last intron/exon boundary is too small

Length of CDS

1773

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

501476

Chromosomal position

239888040

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