Variant rs1533079 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 0.135 in 152,166 control chromosomes in the GnomAD database, including 1,803 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 0.13 ( 1803 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.44

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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.49 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:

0.135

AC:

20470

AN:

152048

Hom.:

1797

Cov.:

show subpopulations

Gnomad AFR

AF:

0.110

Gnomad AMI

AF:

0.0428

Gnomad AMR

AF:

0.107

Gnomad ASJ

AF:

0.0832

Gnomad EAS

AF:

0.506

Gnomad SAS

AF:

0.173

Gnomad FIN

AF:

0.130

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.130

Gnomad OTH

AF:

0.120

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

GnomAD4 genome

AF:

0.135

AC:

20501

AN:

152166

Hom.:

1803

Cov.:

AF XY:

0.138

AC XY:

10290

AN XY:

74392

show subpopulations

Gnomad4 AFR

AF:

0.110

Gnomad4 AMR

AF:

0.108

Gnomad4 ASJ

AF:

0.0832

Gnomad4 EAS

AF:

0.507

Gnomad4 SAS

AF:

0.174

Gnomad4 FIN

AF:

0.130

Gnomad4 NFE

AF:

0.130

Gnomad4 OTH

AF:

0.123

Alfa

AF:

0.121

Hom.:

1617

Bravo

AF:

0.132

Asia WGS

AF:

0.294

AC:

1022

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.45

DANN

Benign

0.29

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