rs2925260

Positions:

• chr15-25624825-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;