chr15-26542936-G-C

Position:

• chr15-26542936-G-C

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 0.464 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.465 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

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.449

Gnomad4 OTH AF: 0.468

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8025575; hg19: chr15-26788083;