rs10520926

Variant names:

• chr5-25325828-T-A
• rs10520926

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.165 in 152,142 control chromosomes in the GnomAD database, including 2,388 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 0.16 (2388 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.292 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: 0.165 AC: 25066 AN: 152024 Hom.: 2377 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.165 AC: 25097 AN: 152142 Hom.: 2388 Cov.: 32 AF XY: 0.173 AC XY: 12835 AN XY: 74396

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.205

Alfa AF: 0.157 Hom.: 243

Bravo AF: 0.172

Asia WGS AF: 0.277 AC: 964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.9
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520926; hg19: chr5-25325937;