rs10516024

Variant names:

• chr5-166762275-G-A
• rs10516024

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 0.0509 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0112 AC: 465 AN: 41554

American (AMR) AF: 0.0880 AC: 1345 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0602 AC: 209 AN: 3472

East Asian (EAS) AF: 0.0988 AC: 510 AN: 5164

South Asian (SAS) AF: 0.0351 AC: 169 AN: 4812

European-Finnish (FIN) AF: 0.140 AC: 1476 AN: 10556

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0500 AC: 3402 AN: 67990

Other (OTH) AF: 0.0522 AC: 110 AN: 2106

Alfa AF: 0.0474 Hom.: 101

Bravo AF: 0.0480

Asia WGS AF: 0.0510 AC: 177 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	16
DANN	Benign	0.70
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs10516024; hg19: chr5-166189280;