chr15-48658080-G-C

Variant names:

• chr15-48658080-G-C
• rs893160

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.531 AC: 22014 AN: 41434

American (AMR) AF: 0.759 AC: 11604 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2703 AN: 3472

East Asian (EAS) AF: 0.859 AC: 4446 AN: 5178

South Asian (SAS) AF: 0.836 AC: 4024 AN: 4812

European-Finnish (FIN) AF: 0.713 AC: 7536 AN: 10568

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.743 AC: 50513 AN: 67984

Other (OTH) AF: 0.724 AC: 1527 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.61
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs893160; hg19: chr15-48950277;