13-30740318-C-A

Variant names:

• chr13-30740318-C-A
• rs3885907
• NM_001629.4:c.71-3742C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001629.4(ALOX5AP):​c.71-3742C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.587 in 152,116 control chromosomes in the GnomAD database, including 26,489 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 0.59 (26489 hom., cov: 33)
• Consequence: ALOX5AP NM_001629.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118
• Publications: 27 publications found

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]

LOC124903146 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.71 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001629.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALOX5AP	NM_001629.4	MANE Select	c.71-3742C>A		intron	N/A	NP_001620.2
	ALOX5AP	NM_001204406.2		c.242-3742C>A		intron	N/A	NP_001191335.1	A0A087WW23

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALOX5AP	ENST00000380490.5	TSL:1 MANE Select	c.71-3742C>A		intron	N/A	ENSP00000369858.3	P20292
	ALOX5AP	ENST00000617770.4	TSL:1	c.242-3742C>A		intron	N/A	ENSP00000479870.1	A0A087WW23
	ALOX5AP	ENST00000892335.1		c.71-3742C>A		intron	N/A	ENSP00000562394.1

Frequencies

GnomAD3 genomes AF: 0.587 AC: 89253 AN: 151998 Hom.: 26465 Cov.: 33

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.602

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.587 AC: 89333 AN: 152116 Hom.: 26489 Cov.: 33 AF XY: 0.594 AC XY: 44170 AN XY: 74354

African (AFR) AF: 0.601 AC: 24946 AN: 41496

American (AMR) AF: 0.636 AC: 9717 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2194 AN: 3472

East Asian (EAS) AF: 0.729 AC: 3778 AN: 5182

South Asian (SAS) AF: 0.715 AC: 3454 AN: 4830

European-Finnish (FIN) AF: 0.551 AC: 5815 AN: 10560

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37356 AN: 67976

Other (OTH) AF: 0.605 AC: 1276 AN: 2110

Alfa AF: 0.564 Hom.: 93803

Bravo AF: 0.598

Asia WGS AF: 0.751 AC: 2613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.91
DANN	Benign	0.34
PhyloP100		-0.12
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3885907; hg19: chr13-31314455;