rs2925260

Variant names:

• chr15-25624825-G-A
• rs2925260

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 0.949 in 152,216 control chromosomes in the GnomAD database, including 68,688 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 0.95 (68688 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.996

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.971 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: 0.949 AC: 144319 AN: 152098 Hom.: 68645 Cov.: 33

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.978

Gnomad ASJ AF: 0.983

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.994

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.977

Gnomad OTH AF: 0.961

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

GnomAD4 genome AF: 0.949 AC: 144419 AN: 152216 Hom.: 68688 Cov.: 33 AF XY: 0.950 AC XY: 70728 AN XY: 74424

Gnomad4 AFR AF: 0.869

Gnomad4 AMR AF: 0.978

Gnomad4 ASJ AF: 0.983

Gnomad4 EAS AF: 0.976

Gnomad4 SAS AF: 0.994

Gnomad4 FIN AF: 0.985

Gnomad4 NFE AF: 0.977

Gnomad4 OTH AF: 0.961

Alfa AF: 0.974 Hom.: 85792

Bravo AF: 0.945

Asia WGS AF: 0.984 AC: 3421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	12
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2925260; hg19: chr15-25869972;