chr15-26178900-C-G

Position:

• chr15-26178900-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 0.322 in 151,810 control chromosomes in the GnomAD database, including 8,222 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 0.32 (8222 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48754 AN: 151692 Hom.: 8202 Cov.: 31

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.322 AC: 48817 AN: 151810 Hom.: 8222 Cov.: 31 AF XY: 0.330 AC XY: 24483 AN XY: 74184

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.570

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.322

Alfa AF: 0.116 Hom.: 155

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.11
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs547843; hg19: chr15-26424047;