15-25662543-C-T

Variant names:

• chr15-25662543-C-T
• rs9806558

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 0.34 in 151,852 control chromosomes in the GnomAD database, including 9,166 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 0.34 (9166 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.504 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: 0.340 AC: 51599 AN: 151734 Hom.: 9157 Cov.: 31

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.340 AC: 51630 AN: 151852 Hom.: 9166 Cov.: 31 AF XY: 0.339 AC XY: 25168 AN XY: 74214

African (AFR) AF: 0.293 AC: 12149 AN: 41406

American (AMR) AF: 0.470 AC: 7175 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1115 AN: 3470

East Asian (EAS) AF: 0.520 AC: 2662 AN: 5116

South Asian (SAS) AF: 0.186 AC: 892 AN: 4808

European-Finnish (FIN) AF: 0.354 AC: 3727 AN: 10536

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.335 AC: 22780 AN: 67956

Other (OTH) AF: 0.350 AC: 739 AN: 2110

Alfa AF: 0.334 Hom.: 38372

Bravo AF: 0.351

Asia WGS AF: 0.339 AC: 1179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.45
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs9806558; hg19: chr15-25907690;