10-102874717-A-G

Position:

• chr10-102874717-A-G

Variant summary

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

The NM_020682.4(AS3MT):​c.528+56A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0988 in 1,292,182 control chromosomes in the GnomAD database, including 7,057 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 (898 hom., cov: 32)
  • Exomes 𝑓: 0.098 (6159 hom.)
• Consequence: AS3MT NM_020682.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AS3MT	NM_020682.4	c.528+56A>G		intron_variant		ENST00000369880.8
BORCS7-ASMT	NR_037644.1	n.933+56A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AS3MT	ENST00000369880.8	c.528+56A>G		intron_variant		1	NM_020682.4	P1

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16280 AN: 152072 Hom.: 897 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.0164

Gnomad SAS AF: 0.0617

Gnomad FIN AF: 0.0701

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.109

GnomAD4 exome AF: 0.0977 AC: 111360 AN: 1139992 Hom.: 6159 AF XY: 0.0969 AC XY: 55806 AN XY: 575934

Gnomad4 AFR exome AF: 0.124

Gnomad4 AMR exome AF: 0.0987

Gnomad4 ASJ exome AF: 0.117

Gnomad4 EAS exome AF: 0.0158

Gnomad4 SAS exome AF: 0.0667

Gnomad4 FIN exome AF: 0.0667

Gnomad4 NFE exome AF: 0.103

Gnomad4 OTH exome AF: 0.104

GnomAD4 genome AF: 0.107 AC: 16287 AN: 152190 Hom.: 898 Cov.: 32 AF XY: 0.105 AC XY: 7837 AN XY: 74420

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.0162

Gnomad4 SAS AF: 0.0621

Gnomad4 FIN AF: 0.0701

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.107

Alfa AF: 0.110 Hom.: 165

Bravo AF: 0.113

Asia WGS AF: 0.0520 AC: 180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.58

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: rs3740394; hg19: chr10-104634474;