rs4968647

Variant names:

• chr17-63450316-T-C
• rs4968647

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 0.594 in 152,020 control chromosomes in the GnomAD database, including 29,295 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 0.59 (29295 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.413
• Publications: 17 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 (AFR) allele frequency at 95% confidence interval = 0.854 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: 0.594 AC: 90211 AN: 151902 Hom.: 29238 Cov.: 32

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.594 AC: 90326 AN: 152020 Hom.: 29295 Cov.: 32 AF XY: 0.589 AC XY: 43751 AN XY: 74298

African (AFR) AF: 0.862 AC: 35756 AN: 41504

American (AMR) AF: 0.477 AC: 7281 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1684 AN: 3468

East Asian (EAS) AF: 0.168 AC: 866 AN: 5142

South Asian (SAS) AF: 0.500 AC: 2406 AN: 4812

European-Finnish (FIN) AF: 0.554 AC: 5849 AN: 10564

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.510 AC: 34649 AN: 67946

Other (OTH) AF: 0.541 AC: 1142 AN: 2112

Alfa AF: 0.521 Hom.: 35092

Bravo AF: 0.596

Asia WGS AF: 0.415 AC: 1445 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	3.1
DANN	Benign	0.76
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs4968647; hg19: chr17-61527677;