Variant rs6055363 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 0.0882 in 152,366 control chromosomes in the GnomAD database, including 1,289 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

Frequency

Genomes: 𝑓 0.088 ( 1288 hom., cov: 33)

Exomes 𝑓: 0.036 ( 1 hom. )

Consequence

Unknown

Scores

Clinical Significance

association no assertion criteria provided O:1

Conservation

PhyloP100: 0.706

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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.391 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:

0.0882

AC:

13418

AN:

152164

Hom.:

1286

Cov.:

show subpopulations

Gnomad AFR

AF:

0.184

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.105

Gnomad ASJ

AF:

0.0187

Gnomad EAS

AF:

0.404

Gnomad SAS

AF:

0.0565

Gnomad FIN

AF:

0.0269

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0190

Gnomad OTH

AF:

0.0727

GnomAD4 exome

AF:

0.0357

AC:

AN:

Hom.:

AF XY:

0.0400

AC XY:

AN XY:

show subpopulations

Gnomad4 AMR exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.500

Gnomad4 SAS exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0883

AC:

13443

AN:

152282

Hom.:

1288

Cov.:

AF XY:

0.0906

AC XY:

6745

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.184

Gnomad4 AMR

AF:

0.105

Gnomad4 ASJ

AF:

0.0187

Gnomad4 EAS

AF:

0.405

Gnomad4 SAS

AF:

0.0570

Gnomad4 FIN

AF:

0.0269

Gnomad4 NFE

AF:

0.0190

Gnomad4 OTH

AF:

0.0728

Alfa

AF:

0.0585

Hom.:

Bravo

AF:

0.101

Asia WGS

AF:

0.209

AC:

725

AN:

3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Calcium oxalate urolithiasis

Other:1

association, no assertion criteria provided

case-control

Division of Molecular Genetics and Division of Molecular Medicine, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University

Mar 01, 2014

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

3.5

DANN

Benign

0.37

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over