rs9551960

Variant summary

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

The NM_001629.4(ALOX5AP):​c.71-1257G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 150,484 control chromosomes in the GnomAD database, including 18,826 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 0.47 ( 18826 hom., cov: 28)

Consequence

ALOX5AP
NM_001629.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.224
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]

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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=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ALOX5APNM_001629.4 linkuse as main transcriptc.71-1257G>A intron_variant ENST00000380490.5
LOC124903146XR_007063743.1 linkuse as main transcriptn.220+1706C>T intron_variant, non_coding_transcript_variant
ALOX5APNM_001204406.2 linkuse as main transcriptc.242-1257G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ALOX5APENST00000380490.5 linkuse as main transcriptc.71-1257G>A intron_variant 1 NM_001629.4 P1
ALOX5APENST00000617770.4 linkuse as main transcriptc.242-1257G>A intron_variant 1
ALOX5APENST00000479597.1 linkuse as main transcriptn.210+258G>A intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.466
AC:
70113
AN:
150366
Hom.:
18821
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.183
Gnomad AMI
AF:
0.431
Gnomad AMR
AF:
0.531
Gnomad ASJ
AF:
0.555
Gnomad EAS
AF:
0.648
Gnomad SAS
AF:
0.580
Gnomad FIN
AF:
0.567
Gnomad MID
AF:
0.513
Gnomad NFE
AF:
0.581
Gnomad OTH
AF:
0.494
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.466
AC:
70144
AN:
150484
Hom.:
18826
Cov.:
28
AF XY:
0.470
AC XY:
34453
AN XY:
73270
show subpopulations
Gnomad4 AFR
AF:
0.183
Gnomad4 AMR
AF:
0.531
Gnomad4 ASJ
AF:
0.555
Gnomad4 EAS
AF:
0.649
Gnomad4 SAS
AF:
0.582
Gnomad4 FIN
AF:
0.567
Gnomad4 NFE
AF:
0.581
Gnomad4 OTH
AF:
0.497
Alfa
AF:
0.447
Hom.:
2869
Bravo
AF:
0.452
Asia WGS
AF:
0.574
AC:
1995
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
8.9
DANN
Benign
0.73

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.

Other links and lift over

dbSNP: rs9551960; hg19: chr13-31316940; API