rs10516024

chr5-166762275-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 0.0509 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;