15-50270366-C-T

Variant names:

• chr15-50270366-C-T
• rs2187576

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 0.593 in 151,978 control chromosomes in the GnomAD database, including 27,528 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 0.59 (27528 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157

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 = 0.641 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: 0.593 AC: 90119 AN: 151860 Hom.: 27503 Cov.: 31

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.593 AC: 90196 AN: 151978 Hom.: 27528 Cov.: 31 AF XY: 0.583 AC XY: 43326 AN XY: 74294

Gnomad4 AFR AF: 0.648

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.727

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.592

Alfa AF: 0.586 Hom.: 13162

Bravo AF: 0.610

Asia WGS AF: 0.333 AC: 1162 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2187576; hg19: chr15-50562563;