rs2586760

Positions:

• chr18-50836763-G-A

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 0.48 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.701

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.528

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2586760; hg19: chr18-48363133;