rs4917986

Positions:

• chr10-102870424-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.170+213T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,172 control chromosomes in the GnomAD database, including 1,004 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 0.11 (1004 hom., cov: 32)
• Consequence: AS3MT NM_020682.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.478

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AS3MT	NM_020682.4	c.170+213T>C		intron_variant		ENST00000369880.8	NP_065733.2
BORCS7-ASMT	NR_037644.1	n.575+213T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AS3MT	ENST00000369880.8	c.170+213T>C		intron_variant		1	NM_020682.4	ENSP00000358896	P1

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17295 AN: 152054 Hom.: 1002 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.0865

Gnomad SAS AF: 0.0846

Gnomad FIN AF: 0.0738

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.114 AC: 17310 AN: 152172 Hom.: 1004 Cov.: 32 AF XY: 0.113 AC XY: 8374 AN XY: 74372

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.0865

Gnomad4 SAS AF: 0.0853

Gnomad4 FIN AF: 0.0738

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.112

Alfa AF: 0.116 Hom.: 138

Bravo AF: 0.120

Asia WGS AF: 0.0950 AC: 330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.1
DANN	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs4917986; hg19: chr10-104630181;