rs4254165

Variant summary

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

The NM_001629.4(ALOX5AP):​c.71-319A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 151,802 control chromosomes in the GnomAD database, including 7,067 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 0.30 ( 7067 hom., cov: 30)

Consequence

ALOX5AP
NM_001629.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.56
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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ALOX5APNM_001629.4 linkuse as main transcriptc.71-319A>G intron_variant ENST00000380490.5
LOC124903146XR_007063743.1 linkuse as main transcriptn.220+768T>C intron_variant, non_coding_transcript_variant
ALOX5APNM_001204406.2 linkuse as main transcriptc.242-319A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ALOX5APENST00000380490.5 linkuse as main transcriptc.71-319A>G intron_variant 1 NM_001629.4 P1
ALOX5APENST00000617770.4 linkuse as main transcriptc.242-319A>G intron_variant 1
ALOX5APENST00000479597.1 linkuse as main transcriptn.211-319A>G intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.300
AC:
45502
AN:
151684
Hom.:
7049
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.219
Gnomad AMI
AF:
0.152
Gnomad AMR
AF:
0.306
Gnomad ASJ
AF:
0.348
Gnomad EAS
AF:
0.412
Gnomad SAS
AF:
0.322
Gnomad FIN
AF:
0.327
Gnomad MID
AF:
0.304
Gnomad NFE
AF:
0.332
Gnomad OTH
AF:
0.325
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.300
AC:
45558
AN:
151802
Hom.:
7067
Cov.:
30
AF XY:
0.301
AC XY:
22320
AN XY:
74132
show subpopulations
Gnomad4 AFR
AF:
0.220
Gnomad4 AMR
AF:
0.306
Gnomad4 ASJ
AF:
0.348
Gnomad4 EAS
AF:
0.411
Gnomad4 SAS
AF:
0.323
Gnomad4 FIN
AF:
0.327
Gnomad4 NFE
AF:
0.332
Gnomad4 OTH
AF:
0.330
Alfa
AF:
0.319
Hom.:
7914
Bravo
AF:
0.294
Asia WGS
AF:
0.381
AC:
1326
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.010
DANN
Benign
0.70

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: rs4254165; hg19: chr13-31317878; COSMIC: COSV66858324; API