rs2925296

Variant names:

• chr15-25642434-A-G
• rs2925296

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;