NM_000698.5:c.349+779A>G

Variant names:

• chr10-45383460-A-G
• rs745986
• NM_000698.5:c.349+779A>G

Variant summary

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

The NM_000698.5(ALOX5):​c.349+779A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,170 control chromosomes in the GnomAD database, including 3,091 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 0.20 (3091 hom., cov: 33)
• Consequence: ALOX5 NM_000698.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.759
• Publications: 25 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALOX5	NM_000698.5	c.349+779A>G		intron_variant	Intron 2 of 13	ENST00000374391.7	NP_000689.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALOX5	ENST00000374391.7	c.349+779A>G		intron_variant	Intron 2 of 13	1	NM_000698.5	ENSP00000363512.2
ALOX5	ENST00000542434.5	c.349+779A>G		intron_variant	Intron 2 of 12	1		ENSP00000437634.1

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29784 AN: 152052 Hom.: 3088 Cov.: 33

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.196 AC: 29805 AN: 152170 Hom.: 3091 Cov.: 33 AF XY: 0.200 AC XY: 14889 AN XY: 74418

African (AFR) AF: 0.153 AC: 6360 AN: 41526

American (AMR) AF: 0.156 AC: 2392 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 645 AN: 3470

East Asian (EAS) AF: 0.180 AC: 929 AN: 5160

South Asian (SAS) AF: 0.240 AC: 1155 AN: 4818

European-Finnish (FIN) AF: 0.267 AC: 2831 AN: 10586

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14797 AN: 67998

Other (OTH) AF: 0.191 AC: 404 AN: 2114

Alfa AF: 0.207 Hom.: 5070

Bravo AF: 0.183

Asia WGS AF: 0.175 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.18
DANN	Benign	0.30
PhyloP100		-0.76
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: rs745986; hg19: chr10-45878908;