rs4792590

Variant names:

• chr17-8213797-A-G
• rs4792590

Your query was ambiguous. Multiple possible variants found:

• chr17-8213797-A-G
• chr17-8213797-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 0.842 in 152,158 control chromosomes in the GnomAD database, including 54,267 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 0.84 (54267 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.842 AC: 128064 AN: 152040 Hom.: 54214 Cov.: 31

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.842 AC: 128168 AN: 152158 Hom.: 54267 Cov.: 31 AF XY: 0.845 AC XY: 62825 AN XY: 74386

African (AFR) AF: 0.797 AC: 33062 AN: 41504

American (AMR) AF: 0.833 AC: 12707 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2495 AN: 3472

East Asian (EAS) AF: 0.676 AC: 3494 AN: 5172

South Asian (SAS) AF: 0.854 AC: 4121 AN: 4826

European-Finnish (FIN) AF: 0.929 AC: 9842 AN: 10594

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.879 AC: 59804 AN: 68014

Other (OTH) AF: 0.813 AC: 1716 AN: 2112

Alfa AF: 0.861 Hom.: 238167

Bravo AF: 0.833

Asia WGS AF: 0.788 AC: 2742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.21
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs4792590; hg19: chr17-8117115;