rs4792909

Variant names:

• chr17-43721456-G-T
• rs4792909

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 0.501 in 151,912 control chromosomes in the GnomAD database, including 20,733 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 (20733 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.721 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: 0.501 AC: 76051 AN: 151794 Hom.: 20698 Cov.: 32

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.501 AC: 76129 AN: 151912 Hom.: 20733 Cov.: 32 AF XY: 0.503 AC XY: 37370 AN XY: 74256

Gnomad4 AFR AF: 0.728

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.457

Alfa AF: 0.404 Hom.: 11691

Bravo AF: 0.511

Asia WGS AF: 0.349 AC: 1216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4792909; hg19: chr17-41798824;