rs10520893

Variant names:

• chr5-23679273-G-A
• rs10520893

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 0.799 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.615 AC: 25467 AN: 41432

American (AMR) AF: 0.774 AC: 11811 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.939 AC: 3255 AN: 3468

East Asian (EAS) AF: 0.779 AC: 4012 AN: 5152

South Asian (SAS) AF: 0.787 AC: 3796 AN: 4824

European-Finnish (FIN) AF: 0.847 AC: 8925 AN: 10540

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.903 AC: 61392 AN: 67998

Other (OTH) AF: 0.817 AC: 1722 AN: 2108

Alfa AF: 0.828 Hom.: 6893

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10520893; hg19: chr5-23679382;