chr10-102869479-G-C

Position:

• chr10-102869479-G-C

Variant summary

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

The ENST00000369880.8(AS3MT):​c.-114G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0546 in 1,346,796 control chromosomes in the GnomAD database, including 5,243 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 0.14 (1973 hom., cov: 32)
  • Exomes 𝑓: 0.043 (3270 hom.)
• Consequence: AS3MT ENST00000369880.8 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AS3MT	NM_020682.4	c.-114G>C		5_prime_UTR_variant	1/11	ENST00000369880.8	NP_065733.2
BORCS7-ASMT	NR_037644.1	n.407-326G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AS3MT	ENST00000369880.8	c.-114G>C		5_prime_UTR_variant	1/11	1	NM_020682.4	ENSP00000358896	P1

Frequencies

GnomAD3 genomes AF: 0.145 AC: 21898 AN: 151208 Hom.: 1966 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.0849

Gnomad SAS AF: 0.0833

Gnomad FIN AF: 0.0726

Gnomad MID AF: 0.192

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.136

GnomAD4 exome AF: 0.0432 AC: 51616 AN: 1195476 Hom.: 3270 Cov.: 32 AF XY: 0.0462 AC XY: 27463 AN XY: 594730

Gnomad4 AFR exome AF: 0.137

Gnomad4 AMR exome AF: 0.0671

Gnomad4 ASJ exome AF: 0.0769

Gnomad4 EAS exome AF: 0.0839

Gnomad4 SAS exome AF: 0.0559

Gnomad4 FIN exome AF: 0.0687

Gnomad4 NFE exome AF: 0.0342

Gnomad4 OTH exome AF: 0.0654

GnomAD4 genome AF: 0.145 AC: 21927 AN: 151320 Hom.: 1973 Cov.: 32 AF XY: 0.143 AC XY: 10544 AN XY: 73972

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.0845

Gnomad4 SAS AF: 0.0842

Gnomad4 FIN AF: 0.0726

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.135

Alfa AF: 0.133 Hom.: 207

Bravo AF: 0.158

Asia WGS AF: 0.0670 AC: 225 AN: 3360

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.6
DANN	Benign	0.54

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: rs17881215; hg19: chr10-104629236;