15-52754013-C-T

Variant names:

• chr15-52754013-C-T
• rs2440335

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.196 AC: 7736 AN: 39392

American (AMR) AF: 0.549 AC: 8064 AN: 14700

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1583 AN: 3446

East Asian (EAS) AF: 0.545 AC: 2720 AN: 4992

South Asian (SAS) AF: 0.573 AC: 2651 AN: 4628

European-Finnish (FIN) AF: 0.616 AC: 6099 AN: 9906

Middle Eastern (MID) AF: 0.545 AC: 157 AN: 288

European-Non Finnish (NFE) AF: 0.560 AC: 37694 AN: 67266

Other (OTH) AF: 0.456 AC: 927 AN: 2034

Alfa AF: 0.516 Hom.: 30272

Bravo AF: 0.439

Asia WGS AF: 0.472 AC: 1642 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.1
DANN	Benign	0.53
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2440335; hg19: chr15-53046210;