rs7085854

chr10-102890494-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020682.4(AS3MT):c.886-50T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 1,491,920 control chromosomes in the GnomAD database, including 33,502 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 0.21 (3451 hom., cov: 31)
  • Exomes 𝑓: 0.21 (30051 hom.)
• Consequence: AS3MT NM_020682.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291

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:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AS3MT	NM_020682.4	c.886-50T>C		intron_variant		ENST00000369880.8
BORCS7-ASMT	NR_037644.1	n.1291-50T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AS3MT	ENST00000369880.8	c.886-50T>C		intron_variant		1	NM_020682.4	P1

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31777 AN: 151932 Hom.: 3453 Cov.: 31

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.208

GnomAD3 exomes AF: 0.198 AC: 34549 AN: 174644 Hom.: 3573 AF XY: 0.199 AC XY: 18631 AN XY: 93604

Gnomad AFR exome AF: 0.214

Gnomad AMR exome AF: 0.116

Gnomad ASJ exome AF: 0.232

Gnomad EAS exome AF: 0.200

Gnomad SAS exome AF: 0.173

Gnomad FIN exome AF: 0.222

Gnomad NFE exome AF: 0.212

Gnomad OTH exome AF: 0.197

GnomAD4 exome AF: 0.209 AC: 279643 AN: 1339870 Hom.: 30051 Cov.: 20 AF XY: 0.208 AC XY: 137546 AN XY: 662142

Gnomad4 AFR exome AF: 0.218

Gnomad4 AMR exome AF: 0.122

Gnomad4 ASJ exome AF: 0.230

Gnomad4 EAS exome AF: 0.143

Gnomad4 SAS exome AF: 0.171

Gnomad4 FIN exome AF: 0.219

Gnomad4 NFE exome AF: 0.215

Gnomad4 OTH exome AF: 0.209

GnomAD4 genome AF: 0.209 AC: 31795 AN: 152050 Hom.: 3451 Cov.: 31 AF XY: 0.206 AC XY: 15302 AN XY: 74316

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.210

Alfa AF: 0.210 Hom.: 809

Bravo AF: 0.202

Asia WGS AF: 0.169 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	10
Dann	Benign	0.85

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

LitVar

Other links and lift over

dbSNP: rs7085854; hg19: chr10-104650251; COSMIC: COSV54918590; COSMIC: COSV54918590;