15-25667192-T-C

Variant names:

• chr15-25667192-T-C
• rs17636733

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 0.408 in 152,144 control chromosomes in the GnomAD database, including 13,148 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 0.41 (13148 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 14 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 (NFE) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61973 AN: 152026 Hom.: 13139 Cov.: 33

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.408 AC: 62009 AN: 152144 Hom.: 13148 Cov.: 33 AF XY: 0.404 AC XY: 30033 AN XY: 74374

African (AFR) AF: 0.380 AC: 15767 AN: 41524

American (AMR) AF: 0.307 AC: 4698 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1574 AN: 3472

East Asian (EAS) AF: 0.122 AC: 630 AN: 5160

South Asian (SAS) AF: 0.390 AC: 1881 AN: 4822

European-Finnish (FIN) AF: 0.493 AC: 5213 AN: 10572

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30754 AN: 67984

Other (OTH) AF: 0.418 AC: 883 AN: 2114

Alfa AF: 0.425 Hom.: 55500

Bravo AF: 0.390

Asia WGS AF: 0.273 AC: 949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.0
DANN	Benign	0.42
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs17636733; hg19: chr15-25912339;