rs933769

chr15-95509513-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 0.835 in 152,048 control chromosomes in the GnomAD database, including 53,456 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 0.84 (53456 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187

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 (AFR) allele frequency at 95% confidence interval = 0.915 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: 0.835 AC: 126923 AN: 151930 Hom.: 53407 Cov.: 31

Gnomad AFR AF: 0.922

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.822

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.835 AC: 127020 AN: 152048 Hom.: 53456 Cov.: 31 AF XY: 0.832 AC XY: 61796 AN XY: 74308

Gnomad4 AFR AF: 0.922

Gnomad4 AMR AF: 0.801

Gnomad4 ASJ AF: 0.772

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.823

Gnomad4 NFE AF: 0.822

Gnomad4 OTH AF: 0.812

Alfa AF: 0.812 Hom.: 75490

Bravo AF: 0.837

Asia WGS AF: 0.605 AC: 2107 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	1.4
Dann	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs933769; hg19: chr15-96052742;