rs477963

Variant names:

• chr17-74645301-C-T
• rs477963

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 0.0528 in 152,212 control chromosomes in the GnomAD database, including 235 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 0.053 (235 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.758
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0617 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: 0.0528 AC: 8033 AN: 152092 Hom.: 235 Cov.: 32

Gnomad AFR AF: 0.0351

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0518

Gnomad ASJ AF: 0.0418

Gnomad EAS AF: 0.0617

Gnomad SAS AF: 0.0618

Gnomad FIN AF: 0.0520

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0633

Gnomad OTH AF: 0.0623

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

GnomAD4 genome AF: 0.0528 AC: 8030 AN: 152212 Hom.: 235 Cov.: 32 AF XY: 0.0509 AC XY: 3788 AN XY: 74420

African (AFR) AF: 0.0351 AC: 1458 AN: 41518

American (AMR) AF: 0.0517 AC: 790 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0418 AC: 145 AN: 3472

East Asian (EAS) AF: 0.0616 AC: 319 AN: 5176

South Asian (SAS) AF: 0.0612 AC: 295 AN: 4820

European-Finnish (FIN) AF: 0.0520 AC: 551 AN: 10602

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0633 AC: 4303 AN: 68018

Other (OTH) AF: 0.0611 AC: 129 AN: 2110

Alfa AF: 0.0597 Hom.: 524

Bravo AF: 0.0526

Asia WGS AF: 0.0620 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.51
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs477963; hg19: chr17-72641440;