rs7090328

Positions:

• chr10-45422628-A-G
• chr10-45422628-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000698.5(ALOX5):​c.555-1413A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 152,172 control chromosomes in the GnomAD database, including 46,091 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 0.77 (46091 hom., cov: 33)
• Consequence: ALOX5 NM_000698.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

ALOX5 (HGNC:435): (arachidonate 5-lipoxygenase) This gene encodes a member of the lipoxygenase gene family and plays a dual role in the synthesis of leukotrienes from arachidonic acid. The encoded protein, which is expressed specifically in bone marrow-derived cells, catalyzes the conversion of arachidonic acid to 5(S)-hydroperoxy-6-trans-8,11,14-cis-eicosatetraenoic acid, and further to the allylic epoxide 5(S)-trans-7,9-trans-11,14-cis-eicosatetrenoic acid (leukotriene A4). Leukotrienes are important mediators of a number of inflammatory and allergic conditions. Mutations in the promoter region of this gene lead to a diminished response to antileukotriene drugs used in the treatment of asthma and may also be associated with atherosclerosis and several cancers. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALOX5	NM_000698.5	c.555-1413A>G		intron_variant		ENST00000374391.7	NP_000689.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALOX5	ENST00000374391.7	c.555-1413A>G		intron_variant		1	NM_000698.5	ENSP00000363512	P1
ALOX5	ENST00000542434.5	c.555-1413A>G		intron_variant		1		ENSP00000437634

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117635 AN: 152054 Hom.: 46051 Cov.: 33

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.774 AC: 117730 AN: 152172 Hom.: 46091 Cov.: 33 AF XY: 0.773 AC XY: 57539 AN XY: 74388

Gnomad4 AFR AF: 0.870

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.868

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.788

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.741

Alfa AF: 0.719 Hom.: 18631

Bravo AF: 0.780

Asia WGS AF: 0.770 AC: 2676 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	0.039
DANN	Benign	0.38

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

Publications

LitVar

Other links and lift over

dbSNP: rs7090328; hg19: chr10-45918076;