rs10507393

Positions:

• chr13-30753384-T-C
• chr13-30753384-T-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ALOX5AP	NM_001629.4	c.241+1262T>C		intron_variant		ENST00000380490.5
LOC124903146	XR_007063743.1	n.89+2127A>G		intron_variant, non_coding_transcript_variant
ALOX5AP	NM_001204406.2	c.412+1262T>C		intron_variant
ALOX5AP	XM_017020522.3	c.121+1262T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALOX5AP	ENST00000380490.5	c.241+1262T>C		intron_variant		1	NM_001629.4	P1
ALOX5AP	ENST00000617770.4	c.412+1262T>C		intron_variant		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

Gnomad4 AFR AF: 0.0562

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.228

Alfa AF: 0.247 Hom.: 1150

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

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: rs10507393; hg19: chr13-31327521;