dbSNP rs3740394: AS3MT:c.528+56A>G (chr10-102874717-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020682.4(AS3MT):c.528+56A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0988 in 1,292,182 control chromosomes in the GnomAD database, including 7,057 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.11 ( 898 hom., cov: 32)

Exomes 𝑓: 0.098 ( 6159 hom. )

Consequence

AS3MT
NM_020682.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.452

Publications

16 publications found

Variant links:

Genes affected

AS3MT (HGNC:17452): (arsenite methyltransferase) AS3MT catalyzes the transfer of a methyl group from S-adenosyl-L-methionine (AdoMet) to trivalent arsenical and may play a role in arsenic metabolism (Lin et al., 2002 [PubMed 11790780]).[supplied by OMIM, Mar 2008]

AS3MT links:

BORCS7-ASMT (HGNC:49183): (BORCS7-ASMT readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring C10orf32 (chromosome 10 open reading frame 32) and AS3MT (arsenic, +3 oxidation state, methyltransferase) genes. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is therefore unlikely to produce a protein product. [provided by RefSeq, Dec 2010]

BORCS7-ASMT links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AS3MT	NM_020682.4 link	c.528+56A>G		intron_variant	Intron 6 of 10	ENST00000369880.8	NP_065733.2	Q9HBK9-1
BORCS7-ASMT	NR_037644.1 link	n.933+56A>G		intron_variant	Intron 10 of 14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AS3MT	ENST00000369880.8 link	c.528+56A>G		intron_variant	Intron 6 of 10	1	NM_020682.4	ENSP00000358896.3		Q9HBK9-1
BORCS7-ASMT	ENST00000299353.6 link	n.*535+56A>G		intron_variant	Intron 10 of 14	5		ENSP00000299353.5		A0A0B4J1R7

Frequencies

GnomAD3 genomes

AF:

0.107

AC:

16280

AN:

152072

Hom.:

897

Cov.:

show subpopulations

Gnomad AFR

AF:

0.126

Gnomad AMI

AF:

0.111

Gnomad AMR

AF:

0.122

Gnomad ASJ

AF:

0.121

Gnomad EAS

AF:

0.0164

Gnomad SAS

AF:

0.0617

Gnomad FIN

AF:

0.0701

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.107

Gnomad OTH

AF:

0.109

GnomAD4 exome

AF:

0.0977

AC:

111360

AN:

1139992

Hom.:

6159

AF XY:

0.0969

AC XY:

55806

AN XY:

575934

show subpopulations

African (AFR)

AF:

0.124

AC:

3274

AN:

26326

American (AMR)

AF:

0.0987

AC:

3692

AN:

37410

Ashkenazi Jewish (ASJ)

AF:

0.117

AC:

2778

AN:

23796

East Asian (EAS)

AF:

0.0158

AC:

559

AN:

35298

South Asian (SAS)

AF:

0.0667

AC:

4977

AN:

74606

European-Finnish (FIN)

AF:

0.0667

AC:

3338

AN:

50022

Middle Eastern (MID)

AF:

0.188

AC:

950

AN:

5042

European-Non Finnish (NFE)

AF:

0.103

AC:

86604

AN:

837752

Other (OTH)

AF:

0.104

AC:

5188

AN:

49740

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

4839

9678

14518

19357

24196

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.107

AC:

16287

AN:

152190

Hom.:

898

Cov.:

AF XY:

0.105

AC XY:

7837

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.125

AC:

5203

AN:

41498

American (AMR)

AF:

0.122

AC:

1869

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.121

AC:

419

AN:

3470

East Asian (EAS)

AF:

0.0162

AC:

AN:

5184

South Asian (SAS)

AF:

0.0621

AC:

300

AN:

4828

European-Finnish (FIN)

AF:

0.0701

AC:

743

AN:

10606

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.107

AC:

7291

AN:

68002

Other (OTH)

AF:

0.107

AC:

225

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

744

1488

2231

2975

3719

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.111

Hom.:

171

Bravo

AF:

0.113

Asia WGS

AF:

0.0520

AC:

180

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.1

(source)

DANN

Benign

0.58

PhyloP100

-0.45

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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rs3740394

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over