rs752760

chr15-51339282-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 0.564 in 152,026 control chromosomes in the GnomAD database, including 26,882 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 0.56 (26882 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.836 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: 0.564 AC: 85624 AN: 151908 Hom.: 26809 Cov.: 31

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.564 AC: 85757 AN: 152026 Hom.: 26882 Cov.: 31 AF XY: 0.557 AC XY: 41407 AN XY: 74290

Gnomad4 AFR AF: 0.844

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.554

Alfa AF: 0.470 Hom.: 7921

Bravo AF: 0.602

Asia WGS AF: 0.580 AC: 2015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.14
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs752760; hg19: chr15-51631479;