NM_020682.4:c.458+254T>A

Variant names:

• chr10-102873487-T-A
• rs7920657
• NM_020682.4:c.458+254T>A

Variant summary

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

The NM_020682.4(AS3MT):​c.458+254T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 151,938 control chromosomes in the GnomAD database, including 4,804 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 0.25 (4804 hom., cov: 31)
• Consequence: AS3MT NM_020682.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.524
• Publications: 5 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AS3MT	NM_020682.4	c.458+254T>A		intron_variant	Intron 5 of 10	ENST00000369880.8	NP_065733.2
BORCS7-ASMT	NR_037644.1	n.863+254T>A		intron_variant	Intron 9 of 14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AS3MT	ENST00000369880.8	c.458+254T>A		intron_variant	Intron 5 of 10	1	NM_020682.4	ENSP00000358896.3
BORCS7-ASMT	ENST00000299353.6	n.*465+254T>A		intron_variant	Intron 9 of 14	5		ENSP00000299353.5

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37309 AN: 151820 Hom.: 4789 Cov.: 31

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.246 AC: 37359 AN: 151938 Hom.: 4804 Cov.: 31 AF XY: 0.244 AC XY: 18142 AN XY: 74256

African (AFR) AF: 0.228 AC: 9440 AN: 41444

American (AMR) AF: 0.249 AC: 3796 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 855 AN: 3468

East Asian (EAS) AF: 0.425 AC: 2186 AN: 5148

South Asian (SAS) AF: 0.229 AC: 1102 AN: 4806

European-Finnish (FIN) AF: 0.233 AC: 2457 AN: 10538

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16838 AN: 67954

Other (OTH) AF: 0.260 AC: 548 AN: 2110

Alfa AF: 0.141 Hom.: 280

Bravo AF: 0.248

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.4
DANN	Benign	0.85
PhyloP100		0.52

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: rs7920657; hg19: chr10-104633244;