15-62926338-C-T

Variant names:

• chr15-62926338-C-T
• rs902027

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 0.643 in 152,070 control chromosomes in the GnomAD database, including 31,738 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 0.64 (31738 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.425
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.789 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: 0.643 AC: 97715 AN: 151952 Hom.: 31721 Cov.: 31

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.643 AC: 97774 AN: 152070 Hom.: 31738 Cov.: 31 AF XY: 0.642 AC XY: 47728 AN XY: 74332

African (AFR) AF: 0.596 AC: 24685 AN: 41448

American (AMR) AF: 0.615 AC: 9395 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.766 AC: 2658 AN: 3472

East Asian (EAS) AF: 0.810 AC: 4190 AN: 5176

South Asian (SAS) AF: 0.611 AC: 2938 AN: 4806

European-Finnish (FIN) AF: 0.611 AC: 6455 AN: 10566

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45191 AN: 68004

Other (OTH) AF: 0.690 AC: 1455 AN: 2108

Alfa AF: 0.583 Hom.: 3332

Bravo AF: 0.646

Asia WGS AF: 0.720 AC: 2501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.5
DANN	Benign	0.42
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs902027; hg19: chr15-63218537;