chr15-54662666-C-T

Variant names:

• chr15-54662666-C-T
• rs9302185

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 0.69 in 151,928 control chromosomes in the GnomAD database, including 40,974 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 (40974 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.86 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: 0.691 AC: 104834 AN: 151812 Hom.: 40971 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.690 AC: 104854 AN: 151928 Hom.: 40974 Cov.: 31 AF XY: 0.698 AC XY: 51833 AN XY: 74248

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.763

Gnomad4 EAS AF: 0.881

Gnomad4 SAS AF: 0.839

Gnomad4 FIN AF: 0.875

Gnomad4 NFE AF: 0.843

Gnomad4 OTH AF: 0.737

Alfa AF: 0.801 Hom.: 24090

Bravo AF: 0.667

Asia WGS AF: 0.817 AC: 2840 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	0.26
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9302185; hg19: chr15-54954864;