rs2925296

chr15-25642434-A-G

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 0.558 in 152,018 control chromosomes in the GnomAD database, including 25,385 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 0.56 (25385 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84820 AN: 151900 Hom.: 25383 Cov.: 31

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.558 AC: 84852 AN: 152018 Hom.: 25385 Cov.: 31 AF XY: 0.563 AC XY: 41832 AN XY: 74294

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.851

Gnomad4 SAS AF: 0.671

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.572

Alfa AF: 0.619 Hom.: 39900

Bravo AF: 0.549

Asia WGS AF: 0.711 AC: 2470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.21
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2925296; hg19: chr15-25887581;