rs10883795

chr10-102894820-T-Cchr10-102894820-T-G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.99).
• 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/exons	MANE	UniProt
AS3MT	NM_020682.4	c.1020+4142T>C		intron_variant		ENST00000369880.8
BORCS7-ASMT	NR_037644.1	n.1425+4142T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AS3MT	ENST00000369880.8	c.1020+4142T>C		intron_variant		1	NM_020682.4	P1

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

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.312

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

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: rs10883795; hg19: chr10-104654577;