15-25892440-G-T

Variant names:

• chr15-25892440-G-T
• rs1553890

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 0.867 in 151,932 control chromosomes in the GnomAD database, including 57,528 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 0.87 (57528 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.919 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: 0.867 AC: 131645 AN: 151814 Hom.: 57474 Cov.: 30

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.812

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.950

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.925

Gnomad OTH AF: 0.886

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

GnomAD4 genome AF: 0.867 AC: 131756 AN: 151932 Hom.: 57528 Cov.: 30 AF XY: 0.865 AC XY: 64236 AN XY: 74238

African (AFR) AF: 0.760 AC: 31443 AN: 41384

American (AMR) AF: 0.883 AC: 13495 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.950 AC: 3296 AN: 3470

East Asian (EAS) AF: 0.851 AC: 4361 AN: 5124

South Asian (SAS) AF: 0.836 AC: 4018 AN: 4808

European-Finnish (FIN) AF: 0.889 AC: 9382 AN: 10552

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.925 AC: 62888 AN: 67988

Other (OTH) AF: 0.886 AC: 1872 AN: 2112

Alfa AF: 0.910 Hom.: 101620

Bravo AF: 0.860

Asia WGS AF: 0.822 AC: 2861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.37
DANN	Benign	0.42
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1553890; hg19: chr15-26137587;