Variant chr13-30744171-C-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001629.4(ALOX5AP):c.170+12C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 1,611,096 control chromosomes in the GnomAD database, including 174,531 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 0.46 ( 16010 hom., cov: 31)

Exomes 𝑓: 0.46 ( 158521 hom. )

Consequence

ALOX5AP
NM_001629.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.830

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:

LOC124903146 (HGNC:):

LOC124903146 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
ALOX5AP	NM_001629.4 link	c.170+12C>A	intron_variant	ENST00000380490.5	NP_001620.2	P20292
ALOX5AP	NM_001204406.2 link	c.341+12C>A	intron_variant		NP_001191335.1	P20292A0A087WW23
ALOX5AP	XM_017020522.3 link	c.-71+12C>A	intron_variant		XP_016876011.1
LOC124903146	XR_007063743.1 link	n.220+338G>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ALOX5AP	ENST00000380490.5 link	c.170+12C>A	intron_variant		1	NM_001629.4	ENSP00000369858.3	P20292
ALOX5AP	ENST00000617770.4 link	c.341+12C>A	intron_variant		1		ENSP00000479870.1	A0A087WW23
ALOX5AP	ENST00000479597.1 link	n.322C>A	non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes

AF:

0.457

AC:

69321

AN:

151832

Hom.:

16002

Cov.:

show subpopulations

Gnomad AFR

AF:

0.430

Gnomad AMI

AF:

0.361

Gnomad AMR

AF:

0.474

Gnomad ASJ

AF:

0.507

Gnomad EAS

AF:

0.620

Gnomad SAS

AF:

0.584

Gnomad FIN

AF:

0.449

Gnomad MID

AF:

0.459

Gnomad NFE

AF:

0.447

Gnomad OTH

AF:

0.468

GnomAD3 exomes

AF:

0.488

AC:

122159

AN:

250230

Hom.:

30336

AF XY:

0.490

AC XY:

66289

AN XY:

135252

show subpopulations

Gnomad AFR exome

AF:

0.434

Gnomad AMR exome

AF:

0.516

Gnomad ASJ exome

AF:

0.507

Gnomad EAS exome

AF:

0.635

Gnomad SAS exome

AF:

0.567

Gnomad FIN exome

AF:

0.451

Gnomad NFE exome

AF:

0.448

Gnomad OTH exome

AF:

0.484

GnomAD4 exome

AF:

0.463

AC:

675813

AN:

1459148

Hom.:

158521

Cov.:

AF XY:

0.465

AC XY:

337840

AN XY:

726024

show subpopulations

Gnomad4 AFR exome

AF:

0.432

Gnomad4 AMR exome

AF:

0.510

Gnomad4 ASJ exome

AF:

0.506

Gnomad4 EAS exome

AF:

0.640

Gnomad4 SAS exome

AF:

0.566

Gnomad4 FIN exome

AF:

0.457

Gnomad4 NFE exome

AF:

0.446

Gnomad4 OTH exome

AF:

0.478

GnomAD4 genome

AF:

0.457

AC:

69376

AN:

151948

Hom.:

16010

Cov.:

AF XY:

0.464

AC XY:

34418

AN XY:

74252

show subpopulations

Gnomad4 AFR

AF:

0.430

Gnomad4 AMR

AF:

0.474

Gnomad4 ASJ

AF:

0.507

Gnomad4 EAS

AF:

0.620

Gnomad4 SAS

AF:

0.584

Gnomad4 FIN

AF:

0.449

Gnomad4 NFE

AF:

0.447

Gnomad4 OTH

AF:

0.473

Alfa

AF:

0.450

Hom.:

21009

Bravo

AF:

0.457

Asia WGS

AF:

0.614

AC:

2140

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

7.8

DANN

Benign

0.66

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