rs10520714

Variant names:

• chr15-93145233-C-T
• rs10520714
• ENST00000711606.1:n.512+3684C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000711606.1(ENSG00000257060):​n.512+3684C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0317 in 152,274 control chromosomes in the GnomAD database, including 107 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 0.032 (107 hom., cov: 31)
• Consequence: ENSG00000257060 ENST00000711606.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.734
• Publications: 2 publications found

Genes affected

ENSG00000257060 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0317 (4832/152274) while in subpopulation NFE AF = 0.0485 (3300/68024). AF 95% confidence interval is 0.0471. There are 107 homozygotes in GnomAd4. There are 2224 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 107 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927025	XR_007064769.1	n.397+3684C>T		intron_variant	Intron 4 of 4
LOC101927025	XR_243235.4	n.500+3684C>T		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257060	ENST00000711606.1	n.512+3684C>T		intron_variant	Intron 5 of 11
ENSG00000257060	ENST00000791023.1	n.203+3684C>T		intron_variant	Intron 2 of 6
ENSG00000257060	ENST00000791051.1	n.416+3684C>T		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes AF: 0.0318 AC: 4832 AN: 152156 Hom.: 107 Cov.: 31

Gnomad AFR AF: 0.00859

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.0331

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0306

Gnomad FIN AF: 0.0170

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0485

Gnomad OTH AF: 0.0373

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

GnomAD4 genome AF: 0.0317 AC: 4832 AN: 152274 Hom.: 107 Cov.: 31 AF XY: 0.0299 AC XY: 2224 AN XY: 74444

African (AFR) AF: 0.00857 AC: 356 AN: 41562

American (AMR) AF: 0.0331 AC: 506 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0481 AC: 167 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5186

South Asian (SAS) AF: 0.0309 AC: 149 AN: 4826

European-Finnish (FIN) AF: 0.0170 AC: 180 AN: 10600

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0485 AC: 3300 AN: 68024

Other (OTH) AF: 0.0369 AC: 78 AN: 2114

Alfa AF: 0.0422 Hom.: 75

Bravo AF: 0.0315

Asia WGS AF: 0.0150 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	0.42
DANN	Benign	0.54
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs10520714; hg19: chr15-93688462;