rs9551963

Variant names:

• chr13-30758410-A-C
• rs9551963
• NM_001629.4:c.323+2385A>C

Your query was ambiguous. Multiple possible variants found:

• chr13-30758410-A-C
• chr13-30758410-A-T

Variant summary

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

The NM_001629.4(ALOX5AP):​c.323+2385A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 152,056 control chromosomes in the GnomAD database, including 19,172 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 0.50 (19172 hom., cov: 31)
• Consequence: ALOX5AP NM_001629.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 31 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALOX5AP	NM_001629.4	c.323+2385A>C		intron_variant	Intron 4 of 4	ENST00000380490.5	NP_001620.2
ALOX5AP	NM_001204406.2	c.494+2385A>C		intron_variant	Intron 5 of 5		NP_001191335.1
ALOX5AP	XM_017020522.3	c.203+2385A>C		intron_variant	Intron 4 of 4		XP_016876011.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALOX5AP	ENST00000380490.5	c.323+2385A>C		intron_variant	Intron 4 of 4	1	NM_001629.4	ENSP00000369858.3
ALOX5AP	ENST00000617770.4	c.494+2385A>C		intron_variant	Intron 5 of 5	1		ENSP00000479870.1

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76064 AN: 151938 Hom.: 19151 Cov.: 31

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.501 AC: 76133 AN: 152056 Hom.: 19172 Cov.: 31 AF XY: 0.497 AC XY: 36944 AN XY: 74338

African (AFR) AF: 0.484 AC: 20076 AN: 41482

American (AMR) AF: 0.549 AC: 8389 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1716 AN: 3470

East Asian (EAS) AF: 0.375 AC: 1934 AN: 5164

South Asian (SAS) AF: 0.399 AC: 1927 AN: 4826

European-Finnish (FIN) AF: 0.526 AC: 5554 AN: 10562

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34784 AN: 67952

Other (OTH) AF: 0.491 AC: 1036 AN: 2108

Alfa AF: 0.503 Hom.: 22652

Bravo AF: 0.504

Asia WGS AF: 0.378 AC: 1313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.17
DANN	Benign	0.31
PhyloP100		-1.9
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: rs9551963; hg19: chr13-31332547;