rs6504960

Variant names:

• chr17-55376187-C-A
• rs6504960

Your query was ambiguous. Multiple possible variants found:

• chr17-55376187-C-A
• chr17-55376187-C-T

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 0.688 in 152,118 control chromosomes in the GnomAD database, including 37,611 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 0.69 (37611 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.89 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: 0.688 AC: 104533 AN: 152000 Hom.: 37588 Cov.: 32

Gnomad AFR AF: 0.898

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.688 AC: 104598 AN: 152118 Hom.: 37611 Cov.: 32 AF XY: 0.691 AC XY: 51389 AN XY: 74338

African (AFR) AF: 0.898 AC: 37304 AN: 41562

American (AMR) AF: 0.636 AC: 9722 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2193 AN: 3454

East Asian (EAS) AF: 0.864 AC: 4461 AN: 5162

South Asian (SAS) AF: 0.817 AC: 3934 AN: 4814

European-Finnish (FIN) AF: 0.592 AC: 6250 AN: 10566

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38588 AN: 67956

Other (OTH) AF: 0.668 AC: 1410 AN: 2110

Alfa AF: 0.508 Hom.: 1467

Bravo AF: 0.698

Asia WGS AF: 0.788 AC: 2739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.75
DANN	Benign	0.52
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs6504960; hg19: chr17-53453548;