rs5761936

Variant names:

• chr22-27064831-G-A
• rs5761936

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 0.163 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.120 AC: 5002 AN: 41542

American (AMR) AF: 0.227 AC: 3471 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 664 AN: 3472

East Asian (EAS) AF: 0.323 AC: 1671 AN: 5166

South Asian (SAS) AF: 0.220 AC: 1061 AN: 4824

European-Finnish (FIN) AF: 0.163 AC: 1729 AN: 10586

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10443 AN: 68008

Other (OTH) AF: 0.188 AC: 397 AN: 2110

Alfa AF: 0.160 Hom.: 4149

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
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs5761936; hg19: chr22-27460793;