rs10883797

Variant names:

• chr10-102899925-T-C
• rs10883797
• NM_020682.4:c.1021-668T>C

Variant summary

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

The NM_020682.4(AS3MT):​c.1021-668T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,006 control chromosomes in the GnomAD database, including 7,061 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 0.30 (7061 hom., cov: 32)
• Consequence: AS3MT NM_020682.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379

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]

ENSG00000286575 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AS3MT	NM_020682.4	c.1021-668T>C		intron_variant	Intron 10 of 10	ENST00000369880.8	NP_065733.2
BORCS7-ASMT	NR_037644.1	n.1426-668T>C		intron_variant	Intron 14 of 14
LOC107984265	NR_160733.1	n.286-453A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AS3MT	ENST00000369880.8	c.1021-668T>C		intron_variant	Intron 10 of 10	1	NM_020682.4	ENSP00000358896.3
BORCS7-ASMT	ENST00000299353.6	n.*1028-668T>C		intron_variant	Intron 14 of 14	5		ENSP00000299353.5
ENSG00000286575	ENST00000652934.1	n.286-453A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45457 AN: 151888 Hom.: 7053 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.299 AC: 45501 AN: 152006 Hom.: 7061 Cov.: 32 AF XY: 0.298 AC XY: 22132 AN XY: 74296

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.280

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.313

Alfa AF: 0.312 Hom.: 925

Bravo AF: 0.295

Asia WGS AF: 0.368 AC: 1278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.76

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: rs10883797; hg19: chr10-104659682;