rs141061806

Variant names:

• chr17-4631894-C-A
• rs141061806
• NM_001140.5:c.1804G>T

Your query was ambiguous. Multiple possible variants found:

• chr17-4631894-C-A
• chr17-4631894-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001140.5(ALOX15):​c.1804G>T​(p.Val602Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ALOX15 NM_001140.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

ALOX15 (HGNC:433): (arachidonate 15-lipoxygenase) This gene encodes a member of the lipoxygenase family of proteins. The encoded enzyme acts on various polyunsaturated fatty acid substrates to generate various bioactive lipid mediators such as eicosanoids, hepoxilins, lipoxins, and other molecules. The encoded enzyme and its reaction products have been shown to regulate inflammation and immunity. Multiple pseudogenes of this gene have been identified in the human genome. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.099931926).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALOX15	NM_001140.5	c.1804G>T	p.Val602Phe	missense_variant	Exon 13 of 14	ENST00000293761.8	NP_001131.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALOX15	ENST00000293761.8	c.1804G>T	p.Val602Phe	missense_variant	Exon 13 of 14	1	NM_001140.5	ENSP00000293761.3
ALOX15	ENST00000570836.6	c.1804G>T	p.Val602Phe	missense_variant	Exon 14 of 15	2		ENSP00000458832.1
ALOX15	ENST00000574640.1	c.1687G>T	p.Val563Phe	missense_variant	Exon 13 of 14	2		ENSP00000460483.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.097
BayesDel_addAF	Benign	-0.10	T
BayesDel_noAF	Benign	-0.39
CADD	Benign	0.0030
DANN	Benign	0.85
DEOGEN2	Benign	0.28	T;T;.
Eigen	Benign	-1.4
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.048	N
LIST_S2	Benign	0.12	.;T;T
M_CAP	Benign	0.0083	T
MetaRNN	Benign	0.10	T;T;T
MetaSVM	Benign	-0.77	T
MutationAssessor	Benign	2.0	M;M;.
PrimateAI	Benign	0.34	T
PROVEAN	Benign	-0.87	.;N;.
REVEL	Benign	0.27
Sift	Benign	0.040	.;D;.
Sift4G	Benign	0.082	T;T;T
Polyphen		0.0060	B;B;.
Vest4		0.17
MVP		0.41
MPC		0.25
ClinPred		0.14	T
GERP RS		-8.7
Varity_R		0.14
gMVP		0.45

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: rs141061806; hg19: chr17-4535189;