rs2925296

Variant names:

• chr15-25642434-A-G
• rs2925296

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 0.558 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.325 AC: 13460 AN: 41466

American (AMR) AF: 0.669 AC: 10210 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2044 AN: 3468

East Asian (EAS) AF: 0.851 AC: 4380 AN: 5144

South Asian (SAS) AF: 0.671 AC: 3235 AN: 4818

European-Finnish (FIN) AF: 0.638 AC: 6748 AN: 10576

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.630 AC: 42843 AN: 67954

Other (OTH) AF: 0.572 AC: 1211 AN: 2116

Alfa AF: 0.610 Hom.: 49317

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
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs2925296; hg19: chr15-25887581;