15-48658080-G-C

Variant names:

• chr15-48658080-G-C
• rs893160

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;