rs10883795

Variant names:

• chr10-102894820-T-C
• rs10883795
• NM_020682.4:c.1020+4142T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-102894820-T-C
• chr10-102894820-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020682.4(AS3MT):​c.1020+4142T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,092 control chromosomes in the GnomAD database, including 7,118 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 0.30 (7118 hom., cov: 32)
• Consequence: AS3MT NM_020682.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.981
• Publications: 11 publications found

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]

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AS3MT	NM_020682.4	c.1020+4142T>C		intron_variant	Intron 10 of 10	ENST00000369880.8	NP_065733.2
BORCS7-ASMT	NR_037644.1	n.1425+4142T>C		intron_variant	Intron 14 of 14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AS3MT	ENST00000369880.8	c.1020+4142T>C		intron_variant	Intron 10 of 10	1	NM_020682.4	ENSP00000358896.3
BORCS7-ASMT	ENST00000299353.6	n.*1027+4142T>C		intron_variant	Intron 14 of 14	5		ENSP00000299353.5

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45621 AN: 151974 Hom.: 7110 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.307

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.300 AC: 45665 AN: 152092 Hom.: 7118 Cov.: 32 AF XY: 0.299 AC XY: 22219 AN XY: 74350

African (AFR) AF: 0.257 AC: 10675 AN: 41488

American (AMR) AF: 0.281 AC: 4288 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1089 AN: 3468

East Asian (EAS) AF: 0.475 AC: 2450 AN: 5160

South Asian (SAS) AF: 0.358 AC: 1726 AN: 4824

European-Finnish (FIN) AF: 0.296 AC: 3128 AN: 10582

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21359 AN: 67986

Other (OTH) AF: 0.312 AC: 656 AN: 2102

Alfa AF: 0.313 Hom.: 930

Bravo AF: 0.296

Asia WGS AF: 0.369 AC: 1281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.89
DANN	Benign	0.35
PhyloP100		-0.98

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

Other links and lift over

dbSNP: rs10883795; hg19: chr10-104654577;