15-26298579-C-G

Position:

• chr15-26298579-C-G

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 0.15 in 152,168 control chromosomes in the GnomAD database, including 1,760 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 0.15 (1760 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22748 AN: 152050 Hom.: 1753 Cov.: 33

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.0866

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.150 AC: 22786 AN: 152168 Hom.: 1760 Cov.: 33 AF XY: 0.151 AC XY: 11208 AN XY: 74394

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.0868

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.152

Alfa AF: 0.0608 Hom.: 61

Bravo AF: 0.148

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.6
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12148430; hg19: chr15-26543726;