15-52754013-C-T

Position:

• chr15-52754013-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 0.463 in 147,552 control chromosomes in the GnomAD database, including 17,751 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 0.46 (17751 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.463 AC: 68271 AN: 147446 Hom.: 17745 Cov.: 24

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.463 AC: 68286 AN: 147552 Hom.: 17751 Cov.: 24 AF XY: 0.468 AC XY: 33569 AN XY: 71770

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.616

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.456

Alfa AF: 0.526 Hom.: 23886

Bravo AF: 0.439

Asia WGS AF: 0.472 AC: 1642 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.1
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: rs2440335; hg19: chr15-53046210;