chr10-102870655-A-T

Variant names:

• chr10-102870655-A-T
• rs17878846
• NM_020682.4:c.170+444A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020682.4(AS3MT):​c.170+444A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0917 in 152,246 control chromosomes in the GnomAD database, including 935 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 0.092 (935 hom., cov: 32)
• Consequence: AS3MT NM_020682.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271
• Publications: 23 publications found

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]

ENSG00000296999 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AS3MT	NM_020682.4	c.170+444A>T		intron_variant	Intron 3 of 10	ENST00000369880.8	NP_065733.2
BORCS7-ASMT	NR_037644.1	n.575+444A>T		intron_variant	Intron 7 of 14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AS3MT	ENST00000369880.8	c.170+444A>T		intron_variant	Intron 3 of 10	1	NM_020682.4	ENSP00000358896.3
BORCS7-ASMT	ENST00000299353.6	n.*177+444A>T		intron_variant	Intron 7 of 14	5		ENSP00000299353.5
ENSG00000296999	ENST00000744161.1	n.87+167T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0917 AC: 13949 AN: 152128 Hom.: 931 Cov.: 32

Gnomad AFR AF: 0.0214

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.0786

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.0958

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.106

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0917 AC: 13958 AN: 152246 Hom.: 935 Cov.: 32 AF XY: 0.0944 AC XY: 7028 AN XY: 74454

African (AFR) AF: 0.0213 AC: 886 AN: 41566

American (AMR) AF: 0.140 AC: 2146 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0786 AC: 273 AN: 3472

East Asian (EAS) AF: 0.281 AC: 1454 AN: 5172

South Asian (SAS) AF: 0.189 AC: 913 AN: 4828

European-Finnish (FIN) AF: 0.0958 AC: 1017 AN: 10612

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 6990 AN: 67988

Other (OTH) AF: 0.109 AC: 230 AN: 2114

Alfa AF: 0.0988 Hom.: 109

Bravo AF: 0.0919

Asia WGS AF: 0.199 AC: 689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.5
DANN	Benign	0.81
PhyloP100		-0.27

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

Other links and lift over

dbSNP: rs17878846; hg19: chr10-104630412;