Variant 13-30713844-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6

The ENST00000617770.4(ALOX5AP):c.116+3G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000981 in 650,680 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.00012 ( 0 hom., cov: 24)

Exomes 𝑓: 0.0011 ( 0 hom. )

Consequence

ALOX5AP
ENST00000617770.4 splice_region, intron

Scores

Splicing: ADA: 0.00008935

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.74

Variant links:

Genes affected

ALOX5AP (HGNC:436): (arachidonate 5-lipoxygenase activating protein) This gene encodes a protein which, with 5-lipoxygenase, is required for leukotriene synthesis. Leukotrienes are arachidonic acid metabolites which have been implicated in various types of inflammatory responses, including asthma, arthritis and psoriasis. This protein localizes to the plasma membrane. Inhibitors of its function impede translocation of 5-lipoxygenase from the cytoplasm to the cell membrane and inhibit 5-lipoxygenase activation. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Feb 2011]

ALOX5AP links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 13-30713844-G-A is Benign according to our data. Variant chr13-30713844-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3041316.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALOX5AP	NM_001204406.2 linkuse as main transcript	c.116+3G>A		splice_region_variant, intron_variant			NP_001191335.1	P20292A0A087WW23

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALOX5AP	ENST00000617770.4 linkuse as main transcript	c.116+3G>A		splice_region_variant, intron_variant		1		ENSP00000479870.1		A0A087WW23

Frequencies

GnomAD3 genomes

AF:

0.000119

AC:

AN:

75632

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000167

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000147

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000545

AC:

AN:

108216

Hom.:

AF XY:

0.000553

AC XY:

AN XY:

59672

show subpopulations

Gnomad AFR exome

AF:

0.000381

Gnomad AMR exome

AF:

0.000932

Gnomad ASJ exome

AF:

0.000144

Gnomad EAS exome

AF:

0.000228

Gnomad SAS exome

AF:

0.000416

Gnomad FIN exome

AF:

0.000211

Gnomad NFE exome

AF:

0.000664

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00109

AC:

629

AN:

575048

Hom.:

Cov.:

AF XY:

0.00102

AC XY:

294

AN XY:

287098

show subpopulations

Gnomad4 AFR exome

AF:

0.000235

Gnomad4 AMR exome

AF:

0.00240

Gnomad4 ASJ exome

AF:

0.00201

Gnomad4 EAS exome

AF:

0.00168

Gnomad4 SAS exome

AF:

0.000503

Gnomad4 FIN exome

AF:

0.000309

Gnomad4 NFE exome

AF:

0.00110

Gnomad4 OTH exome

AF:

0.00135

GnomAD4 genome

AF:

0.000119

AC:

AN:

75632

Hom.:

Cov.:

AF XY:

0.000136

AC XY:

AN XY:

36740

show subpopulations

Gnomad4 AFR

AF:

0.000167

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000147

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.296

Hom.:

3423

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

ALOX5AP-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jul 03, 2019

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

4.1

DANN

Benign

0.54

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000089

dbscSNV1_RF

Benign

0.062

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