Variant rs10751383 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000698.5(ALOX5):c.1273-494A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 154,744 control chromosomes in the GnomAD database, including 25,247 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 0.57 ( 24841 hom., cov: 34)

Exomes 𝑓: 0.55 ( 406 hom. )

Consequence

ALOX5
NM_000698.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.384

Variant links:

Genes affected

ALOX5 (HGNC:435): (arachidonate 5-lipoxygenase) This gene encodes a member of the lipoxygenase gene family and plays a dual role in the synthesis of leukotrienes from arachidonic acid. The encoded protein, which is expressed specifically in bone marrow-derived cells, catalyzes the conversion of arachidonic acid to 5(S)-hydroperoxy-6-trans-8,11,14-cis-eicosatetraenoic acid, and further to the allylic epoxide 5(S)-trans-7,9-trans-11,14-cis-eicosatetrenoic acid (leukotriene A4). Leukotrienes are important mediators of a number of inflammatory and allergic conditions. Mutations in the promoter region of this gene lead to a diminished response to antileukotriene drugs used in the treatment of asthma and may also be associated with atherosclerosis and several cancers. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]

ALOX5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALOX5	NM_000698.5 link	c.1273-494A>C		intron_variant		ENST00000374391.7	NP_000689.1	P09917-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALOX5	ENST00000374391.7 link	c.1273-494A>C		intron_variant		1	NM_000698.5	ENSP00000363512.2		P09917-1
ALOX5	ENST00000542434.5 link	c.1273-494A>C		intron_variant		1		ENSP00000437634.1		P09917-2

Frequencies

GnomAD3 genomes

AF:

0.568

AC:

86355

AN:

152002

Hom.:

24806

Cov.:

show subpopulations

Gnomad AFR

AF:

0.569

Gnomad AMI

AF:

0.538

Gnomad AMR

AF:

0.643

Gnomad ASJ

AF:

0.522

Gnomad EAS

AF:

0.683

Gnomad SAS

AF:

0.442

Gnomad FIN

AF:

0.543

Gnomad MID

AF:

0.585

Gnomad NFE

AF:

0.558

Gnomad OTH

AF:

0.562

GnomAD4 exome

AF:

0.549

AC:

1440

AN:

2624

Hom.:

406

AF XY:

0.558

AC XY:

742

AN XY:

1330

show subpopulations

Gnomad4 AFR exome

AF:

0.481

Gnomad4 AMR exome

AF:

0.625

Gnomad4 ASJ exome

AF:

0.534

Gnomad4 EAS exome

AF:

0.724

Gnomad4 SAS exome

AF:

0.308

Gnomad4 FIN exome

AF:

0.488

Gnomad4 NFE exome

AF:

0.557

Gnomad4 OTH exome

AF:

0.526

GnomAD4 genome

AF:

0.568

AC:

86444

AN:

152120

Hom.:

24841

Cov.:

AF XY:

0.565

AC XY:

42004

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.569

Gnomad4 AMR

AF:

0.643

Gnomad4 ASJ

AF:

0.522

Gnomad4 EAS

AF:

0.683

Gnomad4 SAS

AF:

0.443

Gnomad4 FIN

AF:

0.543

Gnomad4 NFE

AF:

0.558

Gnomad4 OTH

AF:

0.563

Alfa

AF:

0.560

Hom.:

15585

Bravo

AF:

0.581

Asia WGS

AF:

0.555

AC:

1931

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

2.1

DANN

Benign

0.39

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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