10-102900717-G-A

Variant names:

• chr10-102900717-G-A
• rs17879039
• NM_020682.4:c.*17G>A

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_020682.4(AS3MT):​c.*17G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00567 in 1,592,192 control chromosomes in the GnomAD database, including 40 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 0.0048 (3 hom., cov: 31)
  • Exomes 𝑓: 0.0058 (37 hom.)
• Consequence: AS3MT NM_020682.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.49

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]

ENSG00000286575 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS2: High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AS3MT	NM_020682.4	c.*17G>A		3_prime_UTR_variant	Exon 11 of 11	ENST00000369880.8	NP_065733.2
BORCS7-ASMT	NR_037644.1	n.1550G>A		non_coding_transcript_exon_variant	Exon 15 of 15
LOC107984265	NR_160733.1	n.169-207C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AS3MT	ENST00000369880.8	c.*17G>A		3_prime_UTR_variant	Exon 11 of 11	1	NM_020682.4	ENSP00000358896.3
BORCS7-ASMT	ENST00000299353.6	n.*1152G>A		non_coding_transcript_exon_variant	Exon 15 of 15	5		ENSP00000299353.5
BORCS7-ASMT	ENST00000299353.6	n.*1152G>A		3_prime_UTR_variant	Exon 15 of 15	5		ENSP00000299353.5
ENSG00000286575	ENST00000652934.1	n.169-207C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.00485 AC: 738 AN: 152128 Hom.: 3 Cov.: 31

Gnomad AFR AF: 0.00140

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00878

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00601

Gnomad FIN AF: 0.00217

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00675

Gnomad OTH AF: 0.0110

GnomAD2 exomes AF: 0.00551 AC: 1373 AN: 249376 AF XY: 0.00593

Gnomad AFR exome AF: 0.00110

Gnomad AMR exome AF: 0.00551

Gnomad ASJ exome AF: 0.00328

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00163

Gnomad NFE exome AF: 0.00756

Gnomad OTH exome AF: 0.00529

GnomAD4 exome AF: 0.00576 AC: 8297 AN: 1439946 Hom.: 37 Cov.: 26 AF XY: 0.00592 AC XY: 4250 AN XY: 717684

African (AFR) AF: 0.00124 AC: 41 AN: 32974

American (AMR) AF: 0.00519 AC: 232 AN: 44704

Ashkenazi Jewish (ASJ) AF: 0.00346 AC: 90 AN: 26014

East Asian (EAS) AF: 0.00 AC: 0 AN: 39586

South Asian (SAS) AF: 0.00655 AC: 562 AN: 85826

European-Finnish (FIN) AF: 0.00242 AC: 129 AN: 53324

Middle Eastern (MID) AF: 0.00349 AC: 20 AN: 5730

European-Non Finnish (NFE) AF: 0.00632 AC: 6898 AN: 1092186

Other (OTH) AF: 0.00545 AC: 325 AN: 59602

GnomAD4 genome AF: 0.00485 AC: 738 AN: 152246 Hom.: 3 Cov.: 31 AF XY: 0.00480 AC XY: 357 AN XY: 74430

African (AFR) AF: 0.00140 AC: 58 AN: 41550

American (AMR) AF: 0.00877 AC: 134 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00288 AC: 10 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5174

South Asian (SAS) AF: 0.00602 AC: 29 AN: 4820

European-Finnish (FIN) AF: 0.00217 AC: 23 AN: 10606

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00675 AC: 459 AN: 68024

Other (OTH) AF: 0.0109 AC: 23 AN: 2114

Alfa AF: 0.00603 Hom.: 4

Bravo AF: 0.00468

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.1
DANN	Benign	0.49

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: rs17879039; hg19: chr10-104660474;