rs9579648

Variant names:

• chr13-30752895-G-C
• rs9579648
• NM_001629.4:c.241+773G>C

Your query was ambiguous. Multiple possible variants found:

• chr13-30752895-G-C
• chr13-30752895-G-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.241+773G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,214 control chromosomes in the GnomAD database, including 2,444 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 0.18 (2444 hom., cov: 33)
• Consequence: ALOX5AP NM_001629.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.897
• Publications: 15 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALOX5AP	NM_001629.4	c.241+773G>C		intron_variant	Intron 3 of 4	ENST00000380490.5	NP_001620.2
ALOX5AP	NM_001204406.2	c.412+773G>C		intron_variant	Intron 4 of 5		NP_001191335.1
ALOX5AP	XM_017020522.3	c.121+773G>C		intron_variant	Intron 3 of 4		XP_016876011.1
LOC124903146	XR_007063743.1	n.89+2616C>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALOX5AP	ENST00000380490.5	c.241+773G>C		intron_variant	Intron 3 of 4	1	NM_001629.4	ENSP00000369858.3
ALOX5AP	ENST00000617770.4	c.412+773G>C		intron_variant	Intron 4 of 5	1		ENSP00000479870.1

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26663 AN: 152096 Hom.: 2442 Cov.: 33

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0521

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.175 AC: 26689 AN: 152214 Hom.: 2444 Cov.: 33 AF XY: 0.171 AC XY: 12744 AN XY: 74416

African (AFR) AF: 0.180 AC: 7489 AN: 41544

American (AMR) AF: 0.167 AC: 2557 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 583 AN: 3472

East Asian (EAS) AF: 0.109 AC: 563 AN: 5168

South Asian (SAS) AF: 0.0518 AC: 250 AN: 4830

European-Finnish (FIN) AF: 0.200 AC: 2116 AN: 10580

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12445 AN: 68014

Other (OTH) AF: 0.173 AC: 366 AN: 2116

Alfa AF: 0.182 Hom.: 342

Bravo AF: 0.174

Asia WGS AF: 0.0950 AC: 329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.32
DANN	Benign	0.40
PhyloP100		-0.90
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: rs9579648; hg19: chr13-31327032;