rs10516024

Variant names:

• chr5-166762275-G-A
• rs10516024

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 0.0509 in 152,136 control chromosomes in the GnomAD database, including 328 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 0.051 (328 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0917 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: 0.0509 AC: 7734 AN: 152016 Hom.: 328 Cov.: 32

Gnomad AFR AF: 0.0112

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0880

Gnomad ASJ AF: 0.0602

Gnomad EAS AF: 0.0984

Gnomad SAS AF: 0.0347

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0500

Gnomad OTH AF: 0.0533

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

GnomAD4 genome AF: 0.0509 AC: 7738 AN: 152136 Hom.: 328 Cov.: 32 AF XY: 0.0553 AC XY: 4111 AN XY: 74352

Gnomad4 AFR AF: 0.0112

Gnomad4 AMR AF: 0.0880

Gnomad4 ASJ AF: 0.0602

Gnomad4 EAS AF: 0.0988

Gnomad4 SAS AF: 0.0351

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.0500

Gnomad4 OTH AF: 0.0522

Alfa AF: 0.0475 Hom.: 93

Bravo AF: 0.0480

Asia WGS AF: 0.0510 AC: 177 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	16
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516024; hg19: chr5-166189280;