Variant rs6059594 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 0.091 in 152,074 control chromosomes in the GnomAD database, including 1,155 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 0.091 ( 1155 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.740

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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.372 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:

0.0908

AC:

13802

AN:

151954

Hom.:

1143

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0600

Gnomad AMI

AF:

0.0253

Gnomad AMR

AF:

0.208

Gnomad ASJ

AF:

0.0599

Gnomad EAS

AF:

0.385

Gnomad SAS

AF:

0.216

Gnomad FIN

AF:

0.0814

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.0557

Gnomad OTH

AF:

0.0994

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

GnomAD4 genome

AF:

0.0910

AC:

13834

AN:

152074

Hom.:

1155

Cov.:

AF XY:

0.0983

AC XY:

7308

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.0606

Gnomad4 AMR

AF:

0.209

Gnomad4 ASJ

AF:

0.0599

Gnomad4 EAS

AF:

0.386

Gnomad4 SAS

AF:

0.214

Gnomad4 FIN

AF:

0.0814

Gnomad4 NFE

AF:

0.0557

Gnomad4 OTH

AF:

0.0970

Alfa

AF:

0.0641

Hom.:

227

Bravo

AF:

0.0995

Asia WGS

AF:

0.267

AC:

928

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

7.9

DANN

Benign

0.55

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