Variant rs4939583 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.484

Variant links:

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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	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.829

AC:

125984

AN:

151912

Hom.:

53101

Cov.:

show subpopulations

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.:

AF XY:

0.822

AC XY:

61074

AN XY:

74290

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over