rs17879039

chr10-102900717-G-A

Variant summary

Our verdict is Benign. Variant got -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:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AS3MT	NM_020682.4	c.*17G>A		3_prime_UTR_variant	11/11	ENST00000369880.8
BORCS7-ASMT	NR_037644.1	n.1550G>A		non_coding_transcript_exon_variant	15/15
LOC107984265	NR_160733.1	n.169-207C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AS3MT	ENST00000369880.8	c.*17G>A		3_prime_UTR_variant	11/11	1	NM_020682.4	P1
	ENST00000652934.1	n.169-207C>T		intron_variant, non_coding_transcript_variant

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

GnomAD3 exomes AF: 0.00551 AC: 1373 AN: 249376 Hom.: 8 AF XY: 0.00593 AC XY: 802 AN XY: 135322

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 SAS exome AF: 0.00686

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

Gnomad4 AFR exome AF: 0.00124

Gnomad4 AMR exome AF: 0.00519

Gnomad4 ASJ exome AF: 0.00346

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00655

Gnomad4 FIN exome AF: 0.00242

Gnomad4 NFE exome AF: 0.00632

Gnomad4 OTH exome AF: 0.00545

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

Gnomad4 AFR AF: 0.00140

Gnomad4 AMR AF: 0.00877

Gnomad4 ASJ AF: 0.00288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00602

Gnomad4 FIN AF: 0.00217

Gnomad4 NFE AF: 0.00675

Gnomad4 OTH AF: 0.0109

Alfa AF: 0.00522 Hom.: 0

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;