15-86075465-G-A

Variant names:

• chr15-86075465-G-A
• rs2120650

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 0.865 in 152,074 control chromosomes in the GnomAD database, including 57,233 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 0.86 (57233 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.604
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.902 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: 0.865 AC: 131455 AN: 151956 Hom.: 57198 Cov.: 30

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.950

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.865

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.949

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.875

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

GnomAD4 genome AF: 0.865 AC: 131544 AN: 152074 Hom.: 57233 Cov.: 30 AF XY: 0.869 AC XY: 64579 AN XY: 74354

African (AFR) AF: 0.769 AC: 31871 AN: 41452

American (AMR) AF: 0.902 AC: 13787 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.865 AC: 2998 AN: 3466

East Asian (EAS) AF: 0.820 AC: 4219 AN: 5146

South Asian (SAS) AF: 0.816 AC: 3927 AN: 4814

European-Finnish (FIN) AF: 0.949 AC: 10056 AN: 10596

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.908 AC: 61714 AN: 67992

Other (OTH) AF: 0.870 AC: 1839 AN: 2114

Alfa AF: 0.892 Hom.: 261446

Bravo AF: 0.858

Asia WGS AF: 0.806 AC: 2803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.40
DANN	Benign	0.48
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs2120650; hg19: chr15-86618696;