chr17-31812603-G-A

Variant names:

• chr17-31812603-G-A
• rs4795653

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 0.834 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.834 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

African (AFR) AF: 0.906 AC: 37616 AN: 41530

American (AMR) AF: 0.767 AC: 11719 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 2729 AN: 3462

East Asian (EAS) AF: 0.863 AC: 4473 AN: 5184

South Asian (SAS) AF: 0.844 AC: 4074 AN: 4826

European-Finnish (FIN) AF: 0.849 AC: 9007 AN: 10604

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.801 AC: 54508 AN: 68016

Other (OTH) AF: 0.805 AC: 1700 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.1
DANN	Benign	0.60
PhyloP100		-0.027

Splicing

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

Other links and lift over

dbSNP: rs4795653; hg19: chr17-30139622;