rs2586760

Variant names:

• chr18-50836763-G-A
• rs2586760

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 0.48 in 151,868 control chromosomes in the GnomAD database, including 20,477 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 0.48 (20477 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.681 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: 0.481 AC: 72917 AN: 151750 Hom.: 20470 Cov.: 31

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.480 AC: 72922 AN: 151868 Hom.: 20477 Cov.: 31 AF XY: 0.484 AC XY: 35922 AN XY: 74194

African (AFR) AF: 0.170 AC: 7037 AN: 41404

American (AMR) AF: 0.649 AC: 9910 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1974 AN: 3468

East Asian (EAS) AF: 0.460 AC: 2366 AN: 5146

South Asian (SAS) AF: 0.701 AC: 3381 AN: 4824

European-Finnish (FIN) AF: 0.580 AC: 6090 AN: 10498

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.592 AC: 40246 AN: 67940

Other (OTH) AF: 0.528 AC: 1113 AN: 2108

Alfa AF: 0.528 Hom.: 2895

Bravo AF: 0.470

Asia WGS AF: 0.569 AC: 1977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.47
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs2586760; hg19: chr18-48363133;