rs10520893

chr5-23679273-G-A

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 0.799 in 151,988 control chromosomes in the GnomAD database, including 49,814 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 0.80 (49814 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.800 AC: 121469 AN: 151870 Hom.: 49812 Cov.: 32

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.941

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.939

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.903

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.799 AC: 121505 AN: 151988 Hom.: 49814 Cov.: 32 AF XY: 0.795 AC XY: 59108 AN XY: 74318

Gnomad4 AFR AF: 0.615

Gnomad4 AMR AF: 0.774

Gnomad4 ASJ AF: 0.939

Gnomad4 EAS AF: 0.779

Gnomad4 SAS AF: 0.787

Gnomad4 FIN AF: 0.847

Gnomad4 NFE AF: 0.903

Gnomad4 OTH AF: 0.817

Alfa AF: 0.837 Hom.: 6755

Bravo AF: 0.787

Asia WGS AF: 0.743 AC: 2579 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.41
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520893; hg19: chr5-23679382;