17-63473168-C-T

Variant names:

• chr17-63473168-C-T
• rs1800764

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 0.445 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.445 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

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.635

Gnomad4 SAS AF: 0.578

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.546

Gnomad4 OTH AF: 0.452

Alfa AF: 0.519 Hom.: 23266

Bravo AF: 0.432

Asia WGS AF: 0.583 AC: 2027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1800764; hg19: chr17-61550529;