15-25449892-T-C

Variant names:

• chr15-25449892-T-C
• rs780

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 0.664 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.413 AC: 17116 AN: 41406

American (AMR) AF: 0.731 AC: 11156 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2756 AN: 3466

East Asian (EAS) AF: 0.564 AC: 2900 AN: 5142

South Asian (SAS) AF: 0.720 AC: 3465 AN: 4810

European-Finnish (FIN) AF: 0.773 AC: 8159 AN: 10552

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.779 AC: 52952 AN: 67976

Other (OTH) AF: 0.681 AC: 1439 AN: 2112

Alfa AF: 0.749 Hom.: 80079

Bravo AF: 0.651

Asia WGS AF: 0.618 AC: 2154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.8
DANN	Benign	0.72
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs780; hg19: chr15-25695039;