15-45692873-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 0.435 in 151,938 control chromosomes in the GnomAD database, including 14,815 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 (14815 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.898

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.548 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: 0.435 AC: 66016 AN: 151820 Hom.: 14802 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.435 AC: 66068 AN: 151938 Hom.: 14815 Cov.: 32 AF XY: 0.435 AC XY: 32337 AN XY: 74278

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.565

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.443

Alfa AF: 0.451 Hom.: 8215

Bravo AF: 0.422

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.71
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12594515; hg19: chr15-45985071;