rs4795653

Variant names:

• chr17-31812603-G-A
• rs4795653

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 0.834 in 152,220 control chromosomes in the GnomAD database, including 53,121 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 0.83 (53121 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.898 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: 0.834 AC: 126781 AN: 152102 Hom.: 53079 Cov.: 33

Gnomad AFR AF: 0.906

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.808

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

GnomAD4 genome AF: 0.834 AC: 126877 AN: 152220 Hom.: 53121 Cov.: 33 AF XY: 0.836 AC XY: 62224 AN XY: 74420

Gnomad4 AFR AF: 0.906

Gnomad4 AMR AF: 0.767

Gnomad4 ASJ AF: 0.788

Gnomad4 EAS AF: 0.863

Gnomad4 SAS AF: 0.844

Gnomad4 FIN AF: 0.849

Gnomad4 NFE AF: 0.801

Gnomad4 OTH AF: 0.805

Alfa AF: 0.806 Hom.: 11579

Bravo AF: 0.829

Asia WGS AF: 0.854 AC: 2970 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.1
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4795653; hg19: chr17-30139622;