Variant rs4943389 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 0.588 in 151,720 control chromosomes in the GnomAD database, including 26,886 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 0.59 ( 26886 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.111

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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 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:

0.588

AC:

89138

AN:

151602

Hom.:

26874

Cov.:

show subpopulations

Gnomad AFR

AF:

0.528

Gnomad AMI

AF:

0.612

Gnomad AMR

AF:

0.649

Gnomad ASJ

AF:

0.540

Gnomad EAS

AF:

0.933

Gnomad SAS

AF:

0.706

Gnomad FIN

AF:

0.598

Gnomad MID

AF:

0.554

Gnomad NFE

AF:

0.577

Gnomad OTH

AF:

0.569

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

GnomAD4 genome

AF:

0.588

AC:

89196

AN:

151720

Hom.:

26886

Cov.:

AF XY:

0.593

AC XY:

43964

AN XY:

74156

show subpopulations

Gnomad4 AFR

AF:

0.528

Gnomad4 AMR

AF:

0.648

Gnomad4 ASJ

AF:

0.540

Gnomad4 EAS

AF:

0.934

Gnomad4 SAS

AF:

0.706

Gnomad4 FIN

AF:

0.598

Gnomad4 NFE

AF:

0.577

Gnomad4 OTH

AF:

0.567

Alfa

AF:

0.590

Hom.:

6663

Bravo

AF:

0.589

Asia WGS

AF:

0.755

AC:

2625

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

7.2

DANN

Benign

0.52

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