dbSNP rs3740392: AS3MT:c.610+63T>C (chr10-102877098-T-C) – 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.610+63T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 1,481,194 control chromosomes in the GnomAD database, including 47,616 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 0.25 ( 4724 hom., cov: 32)

Exomes 𝑓: 0.25 ( 42892 hom. )

Consequence

AS3MT
NM_020682.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.31

Publications

32 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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AS3MT	NM_020682.4 link	c.610+63T>C		intron_variant	Intron 7 of 10	ENST00000369880.8	NP_065733.2	Q9HBK9-1
BORCS7-ASMT	NR_037644.1 link	n.1015+63T>C		intron_variant	Intron 11 of 14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AS3MT	ENST00000369880.8 link	c.610+63T>C		intron_variant	Intron 7 of 10	1	NM_020682.4	ENSP00000358896.3		Q9HBK9-1
BORCS7-ASMT	ENST00000299353.6 link	n.*617+63T>C		intron_variant	Intron 11 of 14	5		ENSP00000299353.5		A0A0B4J1R7

Frequencies

GnomAD3 genomes

AF:

0.246

AC:

37439

AN:

152114

Hom.:

4722

Cov.:

show subpopulations

Gnomad AFR

AF:

0.223

Gnomad AMI

AF:

0.166

Gnomad AMR

AF:

0.223

Gnomad ASJ

AF:

0.328

Gnomad EAS

AF:

0.283

Gnomad SAS

AF:

0.249

Gnomad FIN

AF:

0.216

Gnomad MID

AF:

0.307

Gnomad NFE

AF:

0.263

Gnomad OTH

AF:

0.255

GnomAD4 exome

AF:

0.251

AC:

333342

AN:

1328962

Hom.:

42892

AF XY:

0.252

AC XY:

167995

AN XY:

667908

show subpopulations

African (AFR)

AF:

0.221

AC:

6796

AN:

30726

American (AMR)

AF:

0.187

AC:

8297

AN:

44404

Ashkenazi Jewish (ASJ)

AF:

0.310

AC:

7801

AN:

25186

East Asian (EAS)

AF:

0.240

AC:

9348

AN:

39030

South Asian (SAS)

AF:

0.241

AC:

20084

AN:

83194

European-Finnish (FIN)

AF:

0.223

AC:

11498

AN:

51668

Middle Eastern (MID)

AF:

0.326

AC:

1793

AN:

5506

European-Non Finnish (NFE)

AF:

0.255

AC:

253319

AN:

993406

Other (OTH)

AF:

0.258

AC:

14406

AN:

55842

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

11894

23788

35681

47575

59469

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.246

AC:

37450

AN:

152232

Hom.:

4724

Cov.:

AF XY:

0.244

AC XY:

18184

AN XY:

74428

show subpopulations

African (AFR)

AF:

0.223

AC:

9278

AN:

41546

American (AMR)

AF:

0.223

AC:

3407

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.328

AC:

1140

AN:

3472

East Asian (EAS)

AF:

0.282

AC:

1463

AN:

5182

South Asian (SAS)

AF:

0.250

AC:

1206

AN:

4830

European-Finnish (FIN)

AF:

0.216

AC:

2287

AN:

10598

Middle Eastern (MID)

AF:

0.313

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.263

AC:

17890

AN:

67990

Other (OTH)

AF:

0.254

AC:

536

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1487

2974

4461

5948

7435

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.255

Hom.:

3717

Bravo

AF:

0.245

Asia WGS

AF:

0.242

AC:

840

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

6.3

(source)

DANN

Benign

0.72

PhyloP100

1.3

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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rs3740392

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