17-63473168-C-T

Variant names:

• chr17-63473168-C-T
• rs1800764

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 0.445 in 151,750 control chromosomes in the GnomAD database, including 17,271 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 0.44 (17271 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.369
• Publications: 72 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67437 AN: 151638 Hom.: 17261 Cov.: 30

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.445 AC: 67457 AN: 151750 Hom.: 17271 Cov.: 30 AF XY: 0.449 AC XY: 33316 AN XY: 74174

African (AFR) AF: 0.169 AC: 7016 AN: 41422

American (AMR) AF: 0.581 AC: 8846 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1579 AN: 3470

East Asian (EAS) AF: 0.635 AC: 3280 AN: 5166

South Asian (SAS) AF: 0.578 AC: 2780 AN: 4810

European-Finnish (FIN) AF: 0.522 AC: 5480 AN: 10504

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.546 AC: 37043 AN: 67844

Other (OTH) AF: 0.452 AC: 954 AN: 2110

Alfa AF: 0.510 Hom.: 56885

Bravo AF: 0.432

Asia WGS AF: 0.583 AC: 2027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.5
DANN	Benign	0.28
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs1800764; hg19: chr17-61550529;