15-32702424-G-T

Variant names:

• chr15-32702424-G-T
• rs12594722

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 0.239 in 152,132 control chromosomes in the GnomAD database, including 4,835 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 0.24 (4835 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.284 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: 0.239 AC: 36326 AN: 152016 Hom.: 4833 Cov.: 33

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.239 AC: 36337 AN: 152132 Hom.: 4835 Cov.: 33 AF XY: 0.239 AC XY: 17734 AN XY: 74346

African (AFR) AF: 0.130 AC: 5391 AN: 41514

American (AMR) AF: 0.291 AC: 4442 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1122 AN: 3468

East Asian (EAS) AF: 0.103 AC: 531 AN: 5176

South Asian (SAS) AF: 0.255 AC: 1231 AN: 4822

European-Finnish (FIN) AF: 0.284 AC: 3001 AN: 10584

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19563 AN: 67972

Other (OTH) AF: 0.250 AC: 529 AN: 2114

Alfa AF: 0.272 Hom.: 6935

Bravo AF: 0.236

Asia WGS AF: 0.196 AC: 679 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.072
DANN	Benign	0.72
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs12594722; hg19: chr15-32994625;