rs10748835

Positions:

• chr10-102900499-G-A

Variant summary

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

The NM_020682.4(AS3MT):​c.1021-94G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 864,272 control chromosomes in the GnomAD database, including 74,789 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 0.41 (12865 hom., cov: 32)
  • Exomes 𝑓: 0.41 (61924 hom.)
• Consequence: AS3MT NM_020682.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AS3MT	NM_020682.4	c.1021-94G>A		intron_variant		ENST00000369880.8
LOC107984265	NR_160733.1	n.180C>T		non_coding_transcript_exon_variant	2/3
BORCS7-ASMT	NR_037644.1	n.1426-94G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AS3MT	ENST00000369880.8	c.1021-94G>A		intron_variant		1	NM_020682.4	P1
	ENST00000652934.1	n.180C>T		non_coding_transcript_exon_variant	2/3

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61975 AN: 151940 Hom.: 12853 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.418

GnomAD4 exome AF: 0.415 AC: 295456 AN: 712214 Hom.: 61924 AF XY: 0.417 AC XY: 155667 AN XY: 373710

Gnomad4 AFR exome AF: 0.380

Gnomad4 AMR exome AF: 0.418

Gnomad4 ASJ exome AF: 0.424

Gnomad4 EAS exome AF: 0.497

Gnomad4 SAS exome AF: 0.457

Gnomad4 FIN exome AF: 0.372

Gnomad4 NFE exome AF: 0.408

Gnomad4 OTH exome AF: 0.418

GnomAD4 genome AF: 0.408 AC: 62031 AN: 152058 Hom.: 12865 Cov.: 32 AF XY: 0.406 AC XY: 30178 AN XY: 74322

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.422

Alfa AF: 0.421 Hom.: 2828

Bravo AF: 0.409

Asia WGS AF: 0.467 AC: 1621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.38

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: rs10748835; hg19: chr10-104660256;