15-45328787-C-T

Position:

• chr15-45328787-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 0.432 in 151,560 control chromosomes in the GnomAD database, including 17,511 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 0.43 (17511 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.45328787C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65317 AN: 151442 Hom.: 17449 Cov.: 30

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.432 AC: 65436 AN: 151560 Hom.: 17511 Cov.: 30 AF XY: 0.437 AC XY: 32331 AN XY: 74018

Gnomad4 AFR AF: 0.703

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.835

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.422

Alfa AF: 0.316 Hom.: 4624

Bravo AF: 0.464

Asia WGS AF: 0.610 AC: 2119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.9
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1719247; hg19: chr15-45620985;