chr18-49541576-C-A

Variant names:

• chr18-49541576-C-A
• rs4939583

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 0.829 in 152,030 control chromosomes in the GnomAD database, including 53,151 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 0.83 (53151 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.942 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: 0.829 AC: 125984 AN: 151912 Hom.: 53101 Cov.: 31

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.846

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

GnomAD4 genome AF: 0.829 AC: 126081 AN: 152030 Hom.: 53151 Cov.: 31 AF XY: 0.822 AC XY: 61074 AN XY: 74290

Gnomad4 AFR AF: 0.950

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.887

Gnomad4 EAS AF: 0.579

Gnomad4 SAS AF: 0.832

Gnomad4 FIN AF: 0.718

Gnomad4 NFE AF: 0.824

Gnomad4 OTH AF: 0.848

Alfa AF: 0.762 Hom.: 4404

Bravo AF: 0.827

Asia WGS AF: 0.730 AC: 2538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.43
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4939583; hg19: chr18-47067946;