15-50270366-C-T

Variant names:

• chr15-50270366-C-T
• rs2187576

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 0.593 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.593 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

African (AFR) AF: 0.648 AC: 26857 AN: 41452

American (AMR) AF: 0.619 AC: 9449 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.727 AC: 2520 AN: 3468

East Asian (EAS) AF: 0.160 AC: 830 AN: 5172

South Asian (SAS) AF: 0.480 AC: 2316 AN: 4820

European-Finnish (FIN) AF: 0.465 AC: 4908 AN: 10544

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41257 AN: 67938

Other (OTH) AF: 0.592 AC: 1249 AN: 2110

Alfa AF: 0.594 Hom.: 15655

Bravo AF: 0.610

Asia WGS AF: 0.333 AC: 1162 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.56
PhyloP100		-0.16

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2187576;

hg19: chr15-50562563;