rs9551960

Variant names:

• chr13-30742803-G-A
• rs9551960
• NM_001629.4:c.71-1257G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-30742803-G-A
• chr13-30742803-G-C
• chr13-30742803-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.71-1257G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 150,484 control chromosomes in the GnomAD database, including 18,826 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 0.47 (18826 hom., cov: 28)
• Consequence: ALOX5AP NM_001629.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.224
• Publications: 8 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 = 0.63 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALOX5AP	NM_001629.4	c.71-1257G>A		intron_variant	Intron 1 of 4	ENST00000380490.5	NP_001620.2
ALOX5AP	NM_001204406.2	c.242-1257G>A		intron_variant	Intron 2 of 5		NP_001191335.1
LOC124903146	XR_007063743.1	n.220+1706C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALOX5AP	ENST00000380490.5	c.71-1257G>A		intron_variant	Intron 1 of 4	1	NM_001629.4	ENSP00000369858.3
ALOX5AP	ENST00000617770.4	c.242-1257G>A		intron_variant	Intron 2 of 5	1		ENSP00000479870.1
ALOX5AP	ENST00000479597.1	n.210+258G>A		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70113 AN: 150366 Hom.: 18821 Cov.: 28

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.466 AC: 70144 AN: 150484 Hom.: 18826 Cov.: 28 AF XY: 0.470 AC XY: 34453 AN XY: 73270

African (AFR) AF: 0.183 AC: 7511 AN: 40998

American (AMR) AF: 0.531 AC: 7990 AN: 15054

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1919 AN: 3460

East Asian (EAS) AF: 0.649 AC: 3260 AN: 5026

South Asian (SAS) AF: 0.582 AC: 2782 AN: 4778

European-Finnish (FIN) AF: 0.567 AC: 5703 AN: 10054

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.581 AC: 39398 AN: 67822

Other (OTH) AF: 0.497 AC: 1041 AN: 2094

Alfa AF: 0.532 Hom.: 33512

Bravo AF: 0.452

Asia WGS AF: 0.574 AC: 1995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.9
DANN	Benign	0.73
PhyloP100		0.22
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: rs9551960; hg19: chr13-31316940;