rs12767543

chr10-102871906-G-Achr10-102871906-G-C

Variant summary

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

The NM_020682.4(AS3MT):c.171-542G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 151,182 control chromosomes in the GnomAD database, including 4,792 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 (4792 hom., cov: 30)
• Consequence: AS3MT NM_020682.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AS3MT	NM_020682.4	c.171-542G>A		intron_variant		ENST00000369880.8
BORCS7-ASMT	NR_037644.1	n.576-542G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AS3MT	ENST00000369880.8	c.171-542G>A		intron_variant		1	NM_020682.4	P1

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37220 AN: 151062 Hom.: 4777 Cov.: 30

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.0859

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.247 AC: 37271 AN: 151182 Hom.: 4792 Cov.: 30 AF XY: 0.245 AC XY: 18099 AN XY: 73810

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.259

Alfa AF: 0.251 Hom.: 589

Bravo AF: 0.248

Asia WGS AF: 0.281 AC: 973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.63
Dann	Benign	0.46

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs12767543; hg19: chr10-104631663;