chr10-102888092-C-T

Variant names:

• chr10-102888092-C-T
• rs12768205
• NM_020682.4:c.886-2452C>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.886-2452C>T variant causes a intron change. The variant allele was found at a frequency of 0.29 in 164,352 control chromosomes in the GnomAD database, including 7,269 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 (7107 hom., cov: 31)
  • Exomes 𝑓: 0.17 (162 hom.)
• Consequence: AS3MT NM_020682.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.83
• Publications: 7 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]

RPL22P17 (HGNC:36985): (ribosomal protein L22 pseudogene 17)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.458 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.886-2452C>T		intron	N/A	NP_065733.2
	BORCS7-ASMT	NR_037644.1		n.1291-2452C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AS3MT	ENST00000369880.8	TSL:1 MANE Select	c.886-2452C>T		intron	N/A	ENSP00000358896.3
	BORCS7-ASMT	ENST00000299353.6	TSL:5	n.*893-2452C>T		intron	N/A	ENSP00000299353.5
	RPL22P17	ENST00000438729.1	TSL:6	n.97G>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45580 AN: 151802 Hom.: 7099 Cov.: 31

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.307

GnomAD4 exome AF: 0.168 AC: 2085 AN: 12432 Hom.: 162 Cov.: 0 AF XY: 0.159 AC XY: 1167 AN XY: 7362

African (AFR) AF: 0.119 AC: 25 AN: 210

American (AMR) AF: 0.153 AC: 291 AN: 1904

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 27 AN: 162

East Asian (EAS) AF: 0.254 AC: 160 AN: 630

South Asian (SAS) AF: 0.174 AC: 164 AN: 942

European-Finnish (FIN) AF: 0.234 AC: 400 AN: 1710

Middle Eastern (MID) AF: 0.0714 AC: 1 AN: 14

European-Non Finnish (NFE) AF: 0.148 AC: 936 AN: 6320

Other (OTH) AF: 0.150 AC: 81 AN: 540

GnomAD4 genome AF: 0.300 AC: 45624 AN: 151920 Hom.: 7107 Cov.: 31 AF XY: 0.299 AC XY: 22166 AN XY: 74216

African (AFR) AF: 0.257 AC: 10671 AN: 41452

American (AMR) AF: 0.281 AC: 4278 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1089 AN: 3468

East Asian (EAS) AF: 0.474 AC: 2448 AN: 5164

South Asian (SAS) AF: 0.357 AC: 1711 AN: 4794

European-Finnish (FIN) AF: 0.295 AC: 3105 AN: 10540

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21367 AN: 67948

Other (OTH) AF: 0.312 AC: 659 AN: 2110

Alfa AF: 0.311 Hom.: 956

Bravo AF: 0.296

Asia WGS AF: 0.369 AC: 1279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	3.1
DANN	Benign	0.70
PhyloP100		3.8

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: rs12768205; hg19: chr10-104647849;