rs2120650

chr15-86075465-G-Achr15-86075465-G-T

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 0.865 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.865 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

Gnomad4 AFR AF: 0.769

Gnomad4 AMR AF: 0.902

Gnomad4 ASJ AF: 0.865

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.816

Gnomad4 FIN AF: 0.949

Gnomad4 NFE AF: 0.908

Gnomad4 OTH AF: 0.870

Alfa AF: 0.898 Hom.: 126983

Bravo AF: 0.858

Asia WGS AF: 0.806 AC: 2803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.40
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2120650; hg19: chr15-86618696;