18-50840088-C-G

Variant names:

• chr18-50840088-C-G
• rs2586761

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 0.688 in 152,056 control chromosomes in the GnomAD database, including 38,650 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 0.69 (38650 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.891 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: 0.688 AC: 104525 AN: 151936 Hom.: 38637 Cov.: 31

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.688 AC: 104559 AN: 152056 Hom.: 38650 Cov.: 31 AF XY: 0.691 AC XY: 51388 AN XY: 74338

African (AFR) AF: 0.389 AC: 16125 AN: 41446

American (AMR) AF: 0.804 AC: 12286 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2754 AN: 3472

East Asian (EAS) AF: 0.913 AC: 4703 AN: 5152

South Asian (SAS) AF: 0.870 AC: 4198 AN: 4824

European-Finnish (FIN) AF: 0.771 AC: 8169 AN: 10596

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.792 AC: 53798 AN: 67964

Other (OTH) AF: 0.724 AC: 1531 AN: 2114

Alfa AF: 0.651 Hom.: 2231

Bravo AF: 0.676

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.2
DANN	Benign	0.34
PhyloP100		0.0060

Splicing

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

Other links and lift over

dbSNP: rs2586761; hg19: chr18-48366458;