rs4939583

Variant names:

• chr18-49541576-C-A
• rs4939583

Your query was ambiguous. Multiple possible variants found:

• chr18-49541576-C-A
• chr18-49541576-C-G
• chr18-49541576-C-T

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 0.829 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.950 AC: 39422 AN: 41514

American (AMR) AF: 0.668 AC: 10180 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.887 AC: 3080 AN: 3472

East Asian (EAS) AF: 0.579 AC: 2983 AN: 5150

South Asian (SAS) AF: 0.832 AC: 4004 AN: 4812

European-Finnish (FIN) AF: 0.718 AC: 7572 AN: 10546

Middle Eastern (MID) AF: 0.949 AC: 277 AN: 292

European-Non Finnish (NFE) AF: 0.824 AC: 55999 AN: 67972

Other (OTH) AF: 0.848 AC: 1791 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.43
DANN	Benign	0.31
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs4939583; hg19: chr18-47067946;