rs5761936

Variant names:

• chr22-27064831-G-A
• rs5761936

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 0.163 in 152,200 control chromosomes in the GnomAD database, including 2,263 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 0.16 (2263 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.925

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 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: 0.162 AC: 24711 AN: 152084 Hom.: 2254 Cov.: 33

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.163 AC: 24735 AN: 152200 Hom.: 2263 Cov.: 33 AF XY: 0.166 AC XY: 12319 AN XY: 74404

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.188

Alfa AF: 0.161 Hom.: 3018

Bravo AF: 0.168

Asia WGS AF: 0.267 AC: 929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.25
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5761936; hg19: chr22-27460793;