chr18-50840088-C-G

Variant names:

• chr18-50840088-C-G
• rs2586761

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 0.688 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.804

Gnomad4 ASJ AF: 0.793

Gnomad4 EAS AF: 0.913

Gnomad4 SAS AF: 0.870

Gnomad4 FIN AF: 0.771

Gnomad4 NFE AF: 0.792

Gnomad4 OTH AF: 0.724

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2586761; hg19: chr18-48366458;