chr13-104130592-C-A

Variant names:

• chr13-104130592-C-A
• rs10508131
• ENST00000670156.1:n.46-460C>A

Variant summary

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

The ENST00000670156.1(ENSG00000287734):​n.46-460C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0702 in 152,200 control chromosomes in the GnomAD database, including 534 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 0.070 (534 hom., cov: 32)
• Consequence: ENSG00000287734 ENST00000670156.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258
• Publications: 1 publications found

Genes affected

ENSG00000287734 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370340	XR_931689.2	n.46-460C>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287734	ENST00000670156.1	n.46-460C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0702 AC: 10683 AN: 152082 Hom.: 535 Cov.: 32

Gnomad AFR AF: 0.0882

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.0464

Gnomad FIN AF: 0.0327

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0470

Gnomad OTH AF: 0.0632

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

GnomAD4 genome AF: 0.0702 AC: 10692 AN: 152200 Hom.: 534 Cov.: 32 AF XY: 0.0709 AC XY: 5275 AN XY: 74404

African (AFR) AF: 0.0883 AC: 3667 AN: 41544

American (AMR) AF: 0.130 AC: 1988 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0435 AC: 151 AN: 3470

East Asian (EAS) AF: 0.186 AC: 965 AN: 5176

South Asian (SAS) AF: 0.0465 AC: 224 AN: 4822

European-Finnish (FIN) AF: 0.0327 AC: 347 AN: 10598

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0470 AC: 3194 AN: 68014

Other (OTH) AF: 0.0620 AC: 131 AN: 2112

Alfa AF: 0.0635 Hom.: 55

Bravo AF: 0.0817

Asia WGS AF: 0.0860 AC: 299 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.53
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs10508131; hg19: chr13-104782942;