rs3740391

Positions:

• chr10-102878664-A-C

Variant summary

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

The NM_020682.4(AS3MT):​c.742+154A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,132 control chromosomes in the GnomAD database, including 1,266 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 0.13 (1266 hom., cov: 31)
• Consequence: AS3MT NM_020682.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698

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:49183): (BORCS7-ASMT readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring C10orf32 (chromosome 10 open reading frame 32) and AS3MT (arsenic, +3 oxidation state, methyltransferase) genes. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is therefore unlikely to produce a protein product. [provided by RefSeq, Dec 2010]

BORCS7-ASMT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AS3MT	NM_020682.4	c.742+154A>C		intron_variant		ENST00000369880.8	NP_065733.2
BORCS7-ASMT	NR_037644.1	n.1147+154A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AS3MT	ENST00000369880.8	c.742+154A>C		intron_variant		1	NM_020682.4	ENSP00000358896.3
BORCS7-ASMT	ENST00000299353.6	n.*749+154A>C		intron_variant		5		ENSP00000299353.5

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19011 AN: 152014 Hom.: 1265 Cov.: 31

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.0652

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.125 AC: 19018 AN: 152132 Hom.: 1266 Cov.: 31 AF XY: 0.122 AC XY: 9061 AN XY: 74364

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.0652

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.159

Alfa AF: 0.120 Hom.: 164

Bravo AF: 0.130

Asia WGS AF: 0.143 AC: 497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.41
DANN	Benign	0.36

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: rs3740391; hg19: chr10-104638421; COSMIC: COSV54919255;