rs5762174

Variant names:

• chr22-27469383-A-C
• rs5762174

Your query was ambiguous. Multiple possible variants found:

• chr22-27469383-A-C
• chr22-27469383-A-G
• chr22-27469383-A-T

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 0.498 in 151,964 control chromosomes in the GnomAD database, including 20,766 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 0.50 (20766 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.810
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.714 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: 0.498 AC: 75635 AN: 151846 Hom.: 20732 Cov.: 31

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.498 AC: 75723 AN: 151964 Hom.: 20766 Cov.: 31 AF XY: 0.496 AC XY: 36791 AN XY: 74246

African (AFR) AF: 0.720 AC: 29878 AN: 41476

American (AMR) AF: 0.534 AC: 8157 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1777 AN: 3468

East Asian (EAS) AF: 0.667 AC: 3431 AN: 5142

South Asian (SAS) AF: 0.537 AC: 2579 AN: 4804

European-Finnish (FIN) AF: 0.297 AC: 3138 AN: 10568

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.374 AC: 25385 AN: 67926

Other (OTH) AF: 0.497 AC: 1049 AN: 2112

Alfa AF: 0.406 Hom.: 6996

Bravo AF: 0.526

Asia WGS AF: 0.592 AC: 2060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.58
DANN	Benign	0.65
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs5762174; hg19: chr22-27865344;