15-25624825-G-A

Variant names:

• chr15-25624825-G-A
• rs2925260

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 0.949 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.869 AC: 36069 AN: 41500

American (AMR) AF: 0.978 AC: 14970 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.983 AC: 3412 AN: 3472

East Asian (EAS) AF: 0.976 AC: 5038 AN: 5164

South Asian (SAS) AF: 0.994 AC: 4796 AN: 4824

European-Finnish (FIN) AF: 0.985 AC: 10452 AN: 10610

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.977 AC: 66453 AN: 68022

Other (OTH) AF: 0.961 AC: 2033 AN: 2116

Alfa AF: 0.970 Hom.: 103061

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
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs2925260; hg19: chr15-25869972;