rs2120650

Variant names:

• chr15-86075465-G-A
• rs2120650

Your query was ambiguous. Multiple possible variants found:

• chr15-86075465-G-A
• chr15-86075465-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;