chr15-25627862-T-C

Variant names:

• chr15-25627862-T-C
• rs2925256

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 0.94 in 152,226 control chromosomes in the GnomAD database, including 67,591 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 0.94 (67591 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.966

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• 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: 0.940 AC: 143016 AN: 152108 Hom.: 67549 Cov.: 32

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.975

Gnomad ASJ AF: 0.983

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.994

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.976

Gnomad OTH AF: 0.953

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

GnomAD4 genome AF: 0.940 AC: 143115 AN: 152226 Hom.: 67591 Cov.: 32 AF XY: 0.942 AC XY: 70136 AN XY: 74438

Gnomad4 AFR AF: 0.841

Gnomad4 AMR AF: 0.975

Gnomad4 ASJ AF: 0.983

Gnomad4 EAS AF: 0.976

Gnomad4 SAS AF: 0.994

Gnomad4 FIN AF: 0.983

Gnomad4 NFE AF: 0.976

Gnomad4 OTH AF: 0.953

Alfa AF: 0.953 Hom.: 3087

Bravo AF: 0.937

Asia WGS AF: 0.980 AC: 3409 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	0.49
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2925256; hg19: chr15-25873009;