10-102869254-T-C

Variant names:

• chr10-102869254-T-C
• rs12416687
• ENST00000299353.6:n.*9-551T>C

Variant summary

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

The ENST00000299353.6(BORCS7-ASMT):​n.*9-551T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 152,182 control chromosomes in the GnomAD database, including 3,665 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 0.21 (3665 hom., cov: 33)
• Consequence: BORCS7-ASMT ENST00000299353.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202
• Publications: 39 publications found

Genes affected

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]

ENSG00000296999 (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]

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 (NFE) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BORCS7-ASMT	NR_037644.1	n.407-551T>C		intron_variant	Intron 5 of 14
AS3MT	NM_020682.4	c.-339T>C		upstream_gene_variant		ENST00000369880.8	NP_065733.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BORCS7-ASMT	ENST00000299353.6	n.*9-551T>C		intron_variant	Intron 5 of 14	5		ENSP00000299353.5
ENSG00000296999	ENST00000744161.1	n.87+1568A>G		intron_variant	Intron 1 of 2
AS3MT	ENST00000369880.8	c.-339T>C		upstream_gene_variant		1	NM_020682.4	ENSP00000358896.3

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32461 AN: 152064 Hom.: 3665 Cov.: 33

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.213 AC: 32464 AN: 152182 Hom.: 3665 Cov.: 33 AF XY: 0.210 AC XY: 15634 AN XY: 74418

African (AFR) AF: 0.157 AC: 6513 AN: 41540

American (AMR) AF: 0.210 AC: 3213 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 978 AN: 3470

East Asian (EAS) AF: 0.160 AC: 828 AN: 5174

South Asian (SAS) AF: 0.103 AC: 496 AN: 4828

European-Finnish (FIN) AF: 0.220 AC: 2328 AN: 10588

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17388 AN: 67978

Other (OTH) AF: 0.224 AC: 474 AN: 2114

Alfa AF: 0.239 Hom.: 5403

Bravo AF: 0.212

Asia WGS AF: 0.121 AC: 419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.2
DANN	Benign	0.55
PhyloP100		0.20
PromoterAI		-0.15	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs12416687; hg19: chr10-104629011;