15-25449892-T-C

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 0.664 in 151,924 control chromosomes in the GnomAD database, including 35,456 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 0.66 (35456 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.773 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: 0.664 AC: 100849 AN: 151806 Hom.: 35456 Cov.: 30

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.664 AC: 100858 AN: 151924 Hom.: 35456 Cov.: 30 AF XY: 0.665 AC XY: 49380 AN XY: 74252

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.795

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.720

Gnomad4 FIN AF: 0.773

Gnomad4 NFE AF: 0.779

Gnomad4 OTH AF: 0.681

Alfa AF: 0.764 Hom.: 59914

Bravo AF: 0.651

Asia WGS AF: 0.618 AC: 2154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.8
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs780; hg19: chr15-25695039;