15-86058245-C-T

Variant names:

• chr15-86058245-C-T
• rs6496307

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 0.831 in 152,210 control chromosomes in the GnomAD database, including 53,606 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 0.83 (53606 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.55
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.831 AC: 126439 AN: 152092 Hom.: 53587 Cov.: 33

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.950

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.916

Gnomad OTH AF: 0.841

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

GnomAD4 genome AF: 0.831 AC: 126514 AN: 152210 Hom.: 53606 Cov.: 33 AF XY: 0.834 AC XY: 62087 AN XY: 74434

African (AFR) AF: 0.652 AC: 27050 AN: 41468

American (AMR) AF: 0.863 AC: 13211 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.849 AC: 2946 AN: 3472

East Asian (EAS) AF: 0.795 AC: 4119 AN: 5184

South Asian (SAS) AF: 0.818 AC: 3943 AN: 4822

European-Finnish (FIN) AF: 0.950 AC: 10087 AN: 10620

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.916 AC: 62288 AN: 68026

Other (OTH) AF: 0.836 AC: 1763 AN: 2108

Alfa AF: 0.881 Hom.: 156702

Bravo AF: 0.817

Asia WGS AF: 0.799 AC: 2779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.5
DANN	Benign	0.62
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs6496307; hg19: chr15-86601476;