rs4792909

Positions:

• chr17-43721456-G-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;