15-55602360-C-T

Position:

• chr15-55602360-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 0.447 in 151,812 control chromosomes in the GnomAD database, including 16,256 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 0.45 (16256 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.811

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 (EAS) allele frequency at 95% confidence interval = 0.944 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: 0.447 AC: 67856 AN: 151694 Hom.: 16255 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.447 AC: 67870 AN: 151812 Hom.: 16256 Cov.: 32 AF XY: 0.459 AC XY: 34045 AN XY: 74206

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.966

Gnomad4 SAS AF: 0.698

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.422

Alfa AF: 0.407 Hom.: 16123

Bravo AF: 0.444

Asia WGS AF: 0.765 AC: 2659 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	1.4
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7175728; hg19: chr15-55894558;