rs8025575

Variant names:

• chr15-26542936-G-C
• rs8025575

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 0.464 in 151,972 control chromosomes in the GnomAD database, including 16,832 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 0.46 (16832 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70550 AN: 151854 Hom.: 16832 Cov.: 32

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.464 AC: 70582 AN: 151972 Hom.: 16832 Cov.: 32 AF XY: 0.462 AC XY: 34299 AN XY: 74274

African (AFR) AF: 0.566 AC: 23440 AN: 41422

American (AMR) AF: 0.410 AC: 6261 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1269 AN: 3470

East Asian (EAS) AF: 0.205 AC: 1061 AN: 5174

South Asian (SAS) AF: 0.389 AC: 1875 AN: 4818

European-Finnish (FIN) AF: 0.443 AC: 4673 AN: 10544

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30541 AN: 67952

Other (OTH) AF: 0.468 AC: 989 AN: 2112

Alfa AF: 0.449 Hom.: 2072

Bravo AF: 0.467

Asia WGS AF: 0.332 AC: 1155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.59
DANN	Benign	0.42
PhyloP100		-0.090

Splicing

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

Other links and lift over

dbSNP: rs8025575; hg19: chr15-26788083;