rs11191453

Positions:

• chr10-102900095-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.1021-498T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0945 in 152,250 control chromosomes in the GnomAD database, including 882 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 0.094 (882 hom., cov: 32)
• Consequence: AS3MT NM_020682.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.522

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]

(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 (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AS3MT	NM_020682.4	c.1021-498T>C		intron_variant		ENST00000369880.8
BORCS7-ASMT	NR_037644.1	n.1426-498T>C		intron_variant, non_coding_transcript_variant
LOC107984265	NR_160733.1	n.285+299A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AS3MT	ENST00000369880.8	c.1021-498T>C		intron_variant		1	NM_020682.4	P1
	ENST00000652934.1	n.285+299A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0944 AC: 14362 AN: 152132 Hom.: 877 Cov.: 32

Gnomad AFR AF: 0.0590

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.0759

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0908

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0945 AC: 14381 AN: 152250 Hom.: 882 Cov.: 32 AF XY: 0.0963 AC XY: 7168 AN XY: 74438

Gnomad4 AFR AF: 0.0591

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.0709

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.0759

Gnomad4 NFE AF: 0.0909

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0918 Hom.: 88

Bravo AF: 0.0978

Asia WGS AF: 0.200 AC: 692 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	2.3
DANN	Benign	0.66

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: rs11191453; hg19: chr10-104659852;