chr13-30736369-A-C

Variant names:

• chr13-30736369-A-C
• rs9579645
• NM_001629.4:c.70+694A>C

Variant summary

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

The NM_001629.4(ALOX5AP):​c.70+694A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,026 control chromosomes in the GnomAD database, including 5,020 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 0.22 (5020 hom., cov: 32)
• Consequence: ALOX5AP NM_001629.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 6 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 (AFR) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALOX5AP	NM_001629.4	c.70+694A>C		intron_variant	Intron 1 of 4	ENST00000380490.5	NP_001620.2
ALOX5AP	NM_001204406.2	c.241+694A>C		intron_variant	Intron 2 of 5		NP_001191335.1
LOC124903146	XR_007063743.1	n.221-3632T>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALOX5AP	ENST00000380490.5	c.70+694A>C		intron_variant	Intron 1 of 4	1	NM_001629.4	ENSP00000369858.3
ALOX5AP	ENST00000617770.4	c.241+694A>C		intron_variant	Intron 2 of 5	1		ENSP00000479870.1

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33341 AN: 151910 Hom.: 5002 Cov.: 32

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.0685

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.220 AC: 33400 AN: 152026 Hom.: 5020 Cov.: 32 AF XY: 0.218 AC XY: 16188 AN XY: 74332

African (AFR) AF: 0.423 AC: 17504 AN: 41372

American (AMR) AF: 0.207 AC: 3165 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 693 AN: 3472

East Asian (EAS) AF: 0.159 AC: 822 AN: 5180

South Asian (SAS) AF: 0.284 AC: 1369 AN: 4812

European-Finnish (FIN) AF: 0.0685 AC: 726 AN: 10596

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.125 AC: 8496 AN: 67994

Other (OTH) AF: 0.213 AC: 450 AN: 2114

Alfa AF: 0.163 Hom.: 4128

Bravo AF: 0.250

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.8
DANN	Benign	0.42
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: rs9579645; hg19: chr13-31310506;