rs4939583

chr18-49541576-C-Achr18-49541576-C-Gchr18-49541576-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;