10-102869708-T-G

Position:

• chr10-102869708-T-G

Variant summary

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

The NM_020682.4(AS3MT):​c.2-97T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 1,575,006 control chromosomes in the GnomAD database, including 109,722 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 0.39 (11043 hom., cov: 31)
  • Exomes 𝑓: 0.37 (98679 hom.)
• Consequence: AS3MT NM_020682.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AS3MT	NM_020682.4	c.2-97T>G		intron_variant		ENST00000369880.8
BORCS7-ASMT	NR_037644.1	n.407-97T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AS3MT	ENST00000369880.8	c.2-97T>G		intron_variant		1	NM_020682.4	P1

Frequencies

GnomAD3 genomes AF: 0.388 AC: 57110 AN: 147076 Hom.: 11029 Cov.: 31

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.412

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.395

GnomAD4 exome AF: 0.371 AC: 530124 AN: 1427828 Hom.: 98679 Cov.: 36 AF XY: 0.374 AC XY: 265963 AN XY: 710582

Gnomad4 AFR exome AF: 0.374

Gnomad4 AMR exome AF: 0.402

Gnomad4 ASJ exome AF: 0.418

Gnomad4 EAS exome AF: 0.527

Gnomad4 SAS exome AF: 0.447

Gnomad4 FIN exome AF: 0.339

Gnomad4 NFE exome AF: 0.357

Gnomad4 OTH exome AF: 0.391

GnomAD4 genome AF: 0.388 AC: 57166 AN: 147178 Hom.: 11043 Cov.: 31 AF XY: 0.388 AC XY: 27850 AN XY: 71694

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.397

Alfa AF: 0.302 Hom.: 1356

Bravo AF: 0.382

Asia WGS AF: 0.441 AC: 1505 AN: 3424

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.3
DANN	Benign	0.55

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: rs3740400; hg19: chr10-104629465; COSMIC: COSV54916132; COSMIC: COSV54916132;