rs11191425

Variant names:

• chr10-102866213-C-T
• rs11191425
• ENST00000299353.6:n.*8+3281C>T

Variant summary

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

The ENST00000299353.6(BORCS7-ASMT):​n.*8+3281C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,156 control chromosomes in the GnomAD database, including 1,010 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 0.10 (1010 hom., cov: 32)
• Consequence: BORCS7-ASMT ENST00000299353.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290
• Publications: 31 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:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000299353.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BORCS7-ASMT	NR_037644.1		n.406+3281C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BORCS7-ASMT	ENST00000299353.6	TSL:5	n.*8+3281C>T		intron	N/A	ENSP00000299353.5
	ENSG00000296999	ENST00000744161.1		n.483+25G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15722 AN: 152038 Hom.: 1005 Cov.: 32

Gnomad AFR AF: 0.0712

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.0795

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.0846

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0988

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.103 AC: 15738 AN: 152156 Hom.: 1010 Cov.: 32 AF XY: 0.105 AC XY: 7822 AN XY: 74400

African (AFR) AF: 0.0711 AC: 2952 AN: 41526

American (AMR) AF: 0.147 AC: 2238 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0795 AC: 276 AN: 3472

East Asian (EAS) AF: 0.282 AC: 1462 AN: 5176

South Asian (SAS) AF: 0.190 AC: 918 AN: 4828

European-Finnish (FIN) AF: 0.0846 AC: 895 AN: 10580

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

European-Non Finnish (NFE) AF: 0.0988 AC: 6716 AN: 67984

Other (OTH) AF: 0.116 AC: 244 AN: 2110

Alfa AF: 0.102 Hom.: 602

Bravo AF: 0.107

Asia WGS AF: 0.201 AC: 697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	6.4
DANN	Benign	0.85
PhyloP100		-0.29

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11191425;

hg19: chr10-104625970;