15-27680690-C-T

Position:

• chr15-27680690-C-T

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 0.769 in 146,476 control chromosomes in the GnomAD database, including 44,611 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 0.77 (44611 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.566

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.897 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: 0.769 AC: 112532 AN: 146392 Hom.: 44561 Cov.: 26

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.778

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.769 AC: 112622 AN: 146476 Hom.: 44611 Cov.: 26 AF XY: 0.764 AC XY: 54677 AN XY: 71570

Gnomad4 AFR AF: 0.905

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.780

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.772

Gnomad4 NFE AF: 0.743

Gnomad4 OTH AF: 0.734

Alfa AF: 0.746 Hom.: 40214

Bravo AF: 0.779

Asia WGS AF: 0.514 AC: 1785 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.2
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs737051; hg19: chr15-27925836;