10-102878107-G-C

Variant names:

• chr10-102878107-G-C
• rs11191438
• NM_020682.4:c.611-272G>C

Variant summary

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

The NM_020682.4(AS3MT):​c.611-272G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,720 control chromosomes in the GnomAD database, including 12,927 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 (12927 hom., cov: 30)
• Consequence: AS3MT NM_020682.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020682.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AS3MT	NM_020682.4	MANE Select	c.611-272G>C		intron	N/A	NP_065733.2
	BORCS7-ASMT	NR_037644.1		n.1016-272G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AS3MT	ENST00000369880.8	TSL:1 MANE Select	c.611-272G>C		intron	N/A	ENSP00000358896.3
	BORCS7-ASMT	ENST00000299353.6	TSL:5	n.*618-272G>C		intron	N/A	ENSP00000299353.5

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62045 AN: 151600 Hom.: 12914 Cov.: 30

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.409 AC: 62103 AN: 151720 Hom.: 12927 Cov.: 30 AF XY: 0.407 AC XY: 30185 AN XY: 74140

African (AFR) AF: 0.378 AC: 15641 AN: 41346

American (AMR) AF: 0.403 AC: 6129 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1516 AN: 3466

East Asian (EAS) AF: 0.562 AC: 2898 AN: 5160

South Asian (SAS) AF: 0.449 AC: 2157 AN: 4806

European-Finnish (FIN) AF: 0.368 AC: 3866 AN: 10506

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28560 AN: 67930

Other (OTH) AF: 0.422 AC: 887 AN: 2100

Alfa AF: 0.285 Hom.: 744

Bravo AF: 0.410

Asia WGS AF: 0.467 AC: 1621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	8.0
DANN	Benign	0.47
PhyloP100		-0.083

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: rs11191438; hg19: chr10-104637864;