rs174760

Variant names:

• chr22-29304546-C-G
• rs174760

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 0.162 in 152,026 control chromosomes in the GnomAD database, including 2,239 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 (2239 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.203 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: 24653 AN: 151906 Hom.: 2239 Cov.: 31

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.0419

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.162 AC: 24655 AN: 152026 Hom.: 2239 Cov.: 31 AF XY: 0.158 AC XY: 11773 AN XY: 74312

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.0418

Gnomad4 SAS AF: 0.0998

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.173

Alfa AF: 0.179 Hom.: 334

Bravo AF: 0.161

Asia WGS AF: 0.0610 AC: 214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.57
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs174760; hg19: chr22-29700536;