chr15-52713950-C-T

Variant names:

• chr15-52713950-C-T
• rs2017176

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 0.457 in 151,902 control chromosomes in the GnomAD database, including 16,029 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 (16029 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.785
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.508 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: 0.457 AC: 69342 AN: 151784 Hom.: 16000 Cov.: 31

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.457 AC: 69419 AN: 151902 Hom.: 16029 Cov.: 31 AF XY: 0.464 AC XY: 34483 AN XY: 74260

African (AFR) AF: 0.398 AC: 16452 AN: 41382

American (AMR) AF: 0.503 AC: 7680 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1304 AN: 3470

East Asian (EAS) AF: 0.476 AC: 2464 AN: 5174

South Asian (SAS) AF: 0.525 AC: 2529 AN: 4816

European-Finnish (FIN) AF: 0.595 AC: 6276 AN: 10552

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.461 AC: 31350 AN: 67938

Other (OTH) AF: 0.445 AC: 940 AN: 2112

Alfa AF: 0.457 Hom.: 48169

Bravo AF: 0.449

Asia WGS AF: 0.518 AC: 1798 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	0.19
DANN	Benign	0.65
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs2017176; hg19: chr15-53006147;