15-48658080-G-C

Position:

• chr15-48658080-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 0.691 in 152,042 control chromosomes in the GnomAD database, including 37,177 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 0.69 (37177 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.838 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: 0.691 AC: 105013 AN: 151924 Hom.: 37159 Cov.: 32

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.691 AC: 105069 AN: 152042 Hom.: 37177 Cov.: 32 AF XY: 0.694 AC XY: 51602 AN XY: 74312

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.759

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.859

Gnomad4 SAS AF: 0.836

Gnomad4 FIN AF: 0.713

Gnomad4 NFE AF: 0.743

Gnomad4 OTH AF: 0.724

Alfa AF: 0.700 Hom.: 4684

Bravo AF: 0.687

Asia WGS AF: 0.798 AC: 2773 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs893160; hg19: chr15-48950277;