rs10520714

Positions:

• chr15-93145233-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.734

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 107 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.93145233C>T		intergenic_region
LOC101927025	XR_007064769.1	n.397+3684C>T		intron_variant
LOC101927025	XR_243235.4	n.500+3684C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.00857

Gnomad4 AMR AF: 0.0331

Gnomad4 ASJ AF: 0.0481

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0309

Gnomad4 FIN AF: 0.0170

Gnomad4 NFE AF: 0.0485

Gnomad4 OTH AF: 0.0369

Alfa AF: 0.0422 Hom.: 67

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520714; hg19: chr15-93688462;