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: ENST00000274353
Querying Taster for transcript #2: ENST00000524080
MT speed 0.03 s - this script 2.414184 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Prediction problem	Splice site change	Known ClinVar disease mutation	Potential ClinVar disease mutation	Amino acid changes	Variant type	dbSNP ID	Protein length	Features at a glance
ENST00000524080	BHMT	Deleterious	164\|36	without_aae		No				Single base exchange		N/A	Heterozygous in gnomAD
ENST00000274353(MANE Select)	BHMT	Deleterious	165\|35	without_aae		No				Single base exchange		Normal	Heterozygous in gnomAD

MutationT@ster 2025

Variant:

5:79119314C>T_2_ENST00000524080

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Prediction:

DeleteriousPermalink

Summary:

Heterozygous in gnomAD

Model: without_aae
Tree vote: 164|36 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr5:79119314C>T (GRCh38)

Gene symbol

BHMT

Gene constraints

LOEUF: 0.98, LOF (oe): 0.68, misssense (oe): 0.81, synonymous (oe): 0.94 ? (gnomAD)

Ensembl transcript ID

ENST00000524080.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.166+3415C>T
g.7506C>T

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	rs35041410
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	29	2594	2623

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.647	1
	3.884	1
(flanking)	8.914	1

?

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

5

Strand

1

Original gDNA sequence snippet

TCAAACGTCATGCAGACCTTCACCTTCTATGCGAGTGAAGA

Altered gDNA sequence snippet

TCAAACGTCATGCAGACCTTTACCTTCTATGCGAGTGAAGA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MPPVGGKKAK KGILERLNAG EIVIGDGGFV FALEKRGYVK AGPWTPEAAV EHPEAGASII
GVNCHFDPTI SLKTVKLMKE GLEAARLKAH LMSQPLAYHT PDCNKQGFID LPEFPFGLEP
RVATRWDIQK YAREAYNLGV RYIGGCCGFE PYHIRAIAEE LAPERGFLPP ASEKHGSWGS
GLDMHTKPWV RARARKEYWE NLRIASGRPY NPSMSKPDGW GVTKGTAELM QQKEATTEQQ
LKELFEKQKF KSQ*

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

78 / 78

Last intron/exon boundary

655

Theoretical NMD boundary in CDS

527

Length of CDS

762

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

7506

Chromosomal position

79119314

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:

5:79119314C>T_1_ENST00000274353

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Prediction:

DeleteriousPermalink

Summary:

Heterozygous in gnomAD

Model: without_aae
Tree vote: 165|35 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr5:79119314C>T (GRCh38)

Gene symbol

BHMT

Gene constraints

LOEUF: 0.88, LOF (oe): 0.66, misssense (oe): 0.82, synonymous (oe): 0.91 ? (gnomAD)

Ensembl transcript ID

ENST00000274353.10

Genbank transcript ID

NM_001713 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.222C>T
g.7506C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs35041410
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	29	2594	2623

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.647	1
	3.884	1
(flanking)	8.914	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

5

Strand

1

Original gDNA sequence snippet

TCAAACGTCATGCAGACCTTCACCTTCTATGCGAGTGAAGA

Altered gDNA sequence snippet

TCAAACGTCATGCAGACCTTTACCTTCTATGCGAGTGAAGA

Original cDNA sequence snippet

TCAAACGTCATGCAGACCTTCACCTTCTATGCGAGTGAAGA

Altered cDNA sequence snippet

TCAAACGTCATGCAGACCTTTACCTTCTATGCGAGTGAAGA

Wildtype AA sequence

MPPVGGKKAK KGILERLNAG EIVIGDGGFV FALEKRGYVK AGPWTPEAAV EHPEAVRQLH
REFLRAGSNV MQTFTFYASE DKLENRGNYV LEKISGQEVN EAACDIARQV ADEGDALVAG
GVSQTPSYLS CKSETEVKKV FLQQLEVFMK KNVDFLIAEY FEHVEEAVWA VETLIASGKP
VAATMCIGPE GDLHGVPPGE CAVRLVKAGA SIIGVNCHFD PTISLKTVKL MKEGLEAARL
KAHLMSQPLA YHTPDCNKQG FIDLPEFPFG LEPRVATRWD IQKYAREAYN LGVRYIGGCC
GFEPYHIRAI AEELAPERGF LPPASEKHGS WGSGLDMHTK PWVRARARKE YWENLRIASG
RPYNPSMSKP DGWGVTKGTA ELMQQKEATT EQQLKELFEK QKFKSQ*

Mutated AA sequence

MPPVGGKKAK KGILERLNAG EIVIGDGGFV FALEKRGYVK AGPWTPEAAV EHPEAVRQLH
REFLRAGSNV MQTFTFYASE DKLENRGNYV LEKISGQEVN EAACDIARQV ADEGDALVAG
GVSQTPSYLS CKSETEVKKV FLQQLEVFMK KNVDFLIAEY FEHVEEAVWA VETLIASGKP
VAATMCIGPE GDLHGVPPGE CAVRLVKAGA SIIGVNCHFD PTISLKTVKL MKEGLEAARL
KAHLMSQPLA YHTPDCNKQG FIDLPEFPFG LEPRVATRWD IQKYAREAYN LGVRYIGGCC
GFEPYHIRAI AEELAPERGF LPPASEKHGS WGSGLDMHTK PWVRARARKE YWENLRIASG
RPYNPSMSKP DGWGVTKGTA ELMQQKEATT EQQLKELFEK QKFKSQ*

Position of stopcodon in wt / mu CDS

1221 / 1221

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

407 / 407

Position of stopcodon in wt / mu cDNA

1298 / 1298

Position of start ATG in wt / mu cDNA

78 / 78

Last intron/exon boundary

1114

Theoretical NMD boundary in CDS

986

Length of CDS

1221

Coding sequence (CDS) position

222

cDNA position

299

gDNA position

7506

Chromosomal position

79119314

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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