chr13-30753384-T-C

Variant names:

• chr13-30753384-T-C
• rs10507393
• NM_001629.4:c.241+1262T>C

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+1262T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,178 control chromosomes in the GnomAD database, including 5,204 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 0.23 (5204 hom., cov: 33)
• Consequence: ALOX5AP NM_001629.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.422
• Publications: 6 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALOX5AP	NM_001629.4	c.241+1262T>C		intron_variant	Intron 3 of 4	ENST00000380490.5	NP_001620.2
ALOX5AP	NM_001204406.2	c.412+1262T>C		intron_variant	Intron 4 of 5		NP_001191335.1
ALOX5AP	XM_017020522.3	c.121+1262T>C		intron_variant	Intron 3 of 4		XP_016876011.1
LOC124903146	XR_007063743.1	n.89+2127A>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+1262T>C		intron_variant	Intron 3 of 4	1	NM_001629.4	ENSP00000369858.3
ALOX5AP	ENST00000617770.4	c.412+1262T>C		intron_variant	Intron 4 of 5	1		ENSP00000479870.1

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35495 AN: 152058 Hom.: 5210 Cov.: 33

Gnomad AFR AF: 0.0564

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.233 AC: 35491 AN: 152178 Hom.: 5204 Cov.: 33 AF XY: 0.234 AC XY: 17418 AN XY: 74382

African (AFR) AF: 0.0562 AC: 2336 AN: 41558

American (AMR) AF: 0.264 AC: 4042 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 891 AN: 3470

East Asian (EAS) AF: 0.250 AC: 1292 AN: 5172

South Asian (SAS) AF: 0.250 AC: 1208 AN: 4824

European-Finnish (FIN) AF: 0.323 AC: 3419 AN: 10574

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21470 AN: 67974

Other (OTH) AF: 0.228 AC: 481 AN: 2108

Alfa AF: 0.265 Hom.: 1954

Bravo AF: 0.222

Asia WGS AF: 0.201 AC: 697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.8
DANN	Benign	0.54
PhyloP100		0.42
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: rs10507393; hg19: chr13-31327521;