rs5761945

Variant names:

• chr22-27082559-C-T
• rs5761945

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 0.51 in 151,954 control chromosomes in the GnomAD database, including 20,042 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 0.51 (20042 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.575 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: 0.510 AC: 77447 AN: 151834 Hom.: 20000 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.542

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.510 AC: 77540 AN: 151954 Hom.: 20042 Cov.: 32 AF XY: 0.511 AC XY: 37957 AN XY: 74252

African (AFR) AF: 0.581 AC: 24089 AN: 41428

American (AMR) AF: 0.442 AC: 6760 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1650 AN: 3468

East Asian (EAS) AF: 0.457 AC: 2362 AN: 5164

South Asian (SAS) AF: 0.587 AC: 2826 AN: 4816

European-Finnish (FIN) AF: 0.492 AC: 5180 AN: 10538

Middle Eastern (MID) AF: 0.538 AC: 157 AN: 292

European-Non Finnish (NFE) AF: 0.484 AC: 32890 AN: 67950

Other (OTH) AF: 0.520 AC: 1098 AN: 2110

Alfa AF: 0.496 Hom.: 10940

Bravo AF: 0.506

Asia WGS AF: 0.494 AC: 1719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.56
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs5761945; hg19: chr22-27478521;