ENST00000652934.1:n.169-1614G>T

Variant names:

• chr10-102902124-C-A
• rs4568943
• ENST00000652934.1:n.169-1614G>T

Variant summary

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

The ENST00000652934.1(ENSG00000286575):​n.169-1614G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0945 in 152,170 control chromosomes in the GnomAD database, including 882 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 0.095 (882 hom., cov: 32)
• Consequence: ENSG00000286575 ENST00000652934.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331
• Publications: 8 publications found

Genes affected

ENSG00000286575 (HGNC:):

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652934.1. 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
	LOC107984265	NR_160733.1		n.169-1614G>T		intron	N/A
	AS3MT	NM_020682.4	MANE Select	c.*1424C>A		downstream_gene	N/A	NP_065733.2
	BORCS7-ASMT	NR_037644.1		n.*225C>A		downstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286575	ENST00000652934.1		n.169-1614G>T		intron	N/A
	ENSG00000286575	ENST00000769603.1		n.412-1614G>T		intron	N/A
	ENSG00000286575	ENST00000769604.1		n.279-1614G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0945 AC: 14364 AN: 152052 Hom.: 877 Cov.: 32

Gnomad AFR AF: 0.0591

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.0758

Gnomad MID AF: 0.0701

Gnomad NFE AF: 0.0909

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0945 AC: 14383 AN: 152170 Hom.: 882 Cov.: 32 AF XY: 0.0964 AC XY: 7171 AN XY: 74386

African (AFR) AF: 0.0592 AC: 2458 AN: 41522

American (AMR) AF: 0.138 AC: 2114 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0709 AC: 246 AN: 3468

East Asian (EAS) AF: 0.278 AC: 1441 AN: 5180

South Asian (SAS) AF: 0.183 AC: 883 AN: 4814

European-Finnish (FIN) AF: 0.0758 AC: 803 AN: 10588

Middle Eastern (MID) AF: 0.0719 AC: 21 AN: 292

European-Non Finnish (NFE) AF: 0.0909 AC: 6181 AN: 68002

Other (OTH) AF: 0.104 AC: 220 AN: 2116

Alfa AF: 0.0432 Hom.: 38

Bravo AF: 0.0978

Asia WGS AF: 0.200 AC: 692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.7
DANN	Benign	0.81
PhyloP100		-0.33

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4568943; hg19: chr10-104661881;