rs10520937

Variant names:

• chr5-27947644-G-A
• rs10520937

Variant summary

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

The variant allele was found at a frequency of 0.166 in 152,086 control chromosomes in the GnomAD database, including 2,868 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 0.17 (2868 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25253 AN: 151968 Hom.: 2854 Cov.: 32

Gnomad AFR AF: 0.0607

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.166 AC: 25280 AN: 152086 Hom.: 2868 Cov.: 32 AF XY: 0.172 AC XY: 12809 AN XY: 74330

African (AFR) AF: 0.0606 AC: 2516 AN: 41498

American (AMR) AF: 0.346 AC: 5285 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 505 AN: 3468

East Asian (EAS) AF: 0.407 AC: 2103 AN: 5162

South Asian (SAS) AF: 0.254 AC: 1228 AN: 4830

European-Finnish (FIN) AF: 0.132 AC: 1392 AN: 10560

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11562 AN: 67986

Other (OTH) AF: 0.181 AC: 381 AN: 2110

Alfa AF: 0.172 Hom.: 6535

Bravo AF: 0.181

Asia WGS AF: 0.293 AC: 1019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.8
DANN	Benign	0.15
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs10520937; hg19: chr5-27947751;