rs6504960

Positions:

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

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 0.688 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.898

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.635

Gnomad4 EAS AF: 0.864

Gnomad4 SAS AF: 0.817

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.668

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6504960; hg19: chr17-53453548;