chr15-26491361-T-C

Position:

• chr15-26491361-T-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 0.439 in 151,964 control chromosomes in the GnomAD database, including 15,486 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 0.44 (15486 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.902

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.51 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: 0.439 AC: 66649 AN: 151846 Hom.: 15479 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.0877

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.439 AC: 66693 AN: 151964 Hom.: 15486 Cov.: 32 AF XY: 0.434 AC XY: 32268 AN XY: 74282

Gnomad4 AFR AF: 0.357

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.0885

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.456

Alfa AF: 0.484 Hom.: 9414

Bravo AF: 0.427

Asia WGS AF: 0.257 AC: 899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.68
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4572353; hg19: chr15-26736508;