rs3803277

Variant names:

• chr13-30744171-C-A
• rs3803277
• NM_001629.4:c.170+12C>A

Your query was ambiguous. Multiple possible variants found:

• chr13-30744171-C-A
• chr13-30744171-C-G

Variant summary

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

The NM_001629.4(ALOX5AP):​c.170+12C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 1,611,096 control chromosomes in the GnomAD database, including 174,531 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 0.46 (16010 hom., cov: 31)
  • Exomes 𝑓: 0.46 (158521 hom.)
• Consequence: ALOX5AP NM_001629.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 18 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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALOX5AP	NM_001629.4	c.170+12C>A		intron_variant	Intron 2 of 4	ENST00000380490.5	NP_001620.2
ALOX5AP	NM_001204406.2	c.341+12C>A		intron_variant	Intron 3 of 5		NP_001191335.1
ALOX5AP	XM_017020522.3	c.-71+12C>A		intron_variant	Intron 1 of 4		XP_016876011.1
LOC124903146	XR_007063743.1	n.220+338G>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALOX5AP	ENST00000380490.5	c.170+12C>A		intron_variant	Intron 2 of 4	1	NM_001629.4	ENSP00000369858.3
ALOX5AP	ENST00000617770.4	c.341+12C>A		intron_variant	Intron 3 of 5	1		ENSP00000479870.1
ALOX5AP	ENST00000479597.1	n.322C>A		non_coding_transcript_exon_variant	Exon 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69321 AN: 151832 Hom.: 16002 Cov.: 31

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.468

GnomAD2 exomes AF: 0.488 AC: 122159 AN: 250230 AF XY: 0.490

Gnomad AFR exome AF: 0.434

Gnomad AMR exome AF: 0.516

Gnomad ASJ exome AF: 0.507

Gnomad EAS exome AF: 0.635

Gnomad FIN exome AF: 0.451

Gnomad NFE exome AF: 0.448

Gnomad OTH exome AF: 0.484

GnomAD4 exome AF: 0.463 AC: 675813 AN: 1459148 Hom.: 158521 Cov.: 32 AF XY: 0.465 AC XY: 337840 AN XY: 726024

African (AFR) AF: 0.432 AC: 14422 AN: 33412

American (AMR) AF: 0.510 AC: 22755 AN: 44638

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 13193 AN: 26094

East Asian (EAS) AF: 0.640 AC: 25361 AN: 39632

South Asian (SAS) AF: 0.566 AC: 48795 AN: 86206

European-Finnish (FIN) AF: 0.457 AC: 24321 AN: 53266

Middle Eastern (MID) AF: 0.467 AC: 2688 AN: 5750

European-Non Finnish (NFE) AF: 0.446 AC: 495470 AN: 1109886

Other (OTH) AF: 0.478 AC: 28808 AN: 60264

GnomAD4 genome AF: 0.457 AC: 69376 AN: 151948 Hom.: 16010 Cov.: 31 AF XY: 0.464 AC XY: 34418 AN XY: 74252

African (AFR) AF: 0.430 AC: 17824 AN: 41456

American (AMR) AF: 0.474 AC: 7248 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1759 AN: 3468

East Asian (EAS) AF: 0.620 AC: 3191 AN: 5148

South Asian (SAS) AF: 0.584 AC: 2809 AN: 4814

European-Finnish (FIN) AF: 0.449 AC: 4738 AN: 10542

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30342 AN: 67930

Other (OTH) AF: 0.473 AC: 997 AN: 2110

Alfa AF: 0.451 Hom.: 27919

Bravo AF: 0.457

Asia WGS AF: 0.614 AC: 2140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.8
DANN	Benign	0.66
PhyloP100		-0.83
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: rs3803277; hg19: chr13-31318308;