chr17-4631740-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001140.5(ALOX15):c.1849C>T(p.Pro617Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0122 in 1,614,068 control chromosomes in the GnomAD database, including 841 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.014 ( 96 hom., cov: 32)
Exomes 𝑓: 0.012 ( 745 hom. )
Consequence
ALOX15
NM_001140.5 missense
NM_001140.5 missense
Scores
2
12
Clinical Significance
Conservation
PhyloP100: -0.0300
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.001753509).
BP6
?
Variant 17-4631740-G-A is Benign according to our data. Variant chr17-4631740-G-A is described in ClinVar as [Benign]. Clinvar id is 1225468.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0983 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALOX15 | NM_001140.5 | c.1849C>T | p.Pro617Ser | missense_variant | 14/14 | ENST00000293761.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALOX15 | ENST00000293761.8 | c.1849C>T | p.Pro617Ser | missense_variant | 14/14 | 1 | NM_001140.5 | P1 | |
ALOX15 | ENST00000570836.6 | c.1849C>T | p.Pro617Ser | missense_variant | 15/15 | 2 | P1 | ||
ALOX15 | ENST00000574640.1 | c.1732C>T | p.Pro578Ser | missense_variant | 14/14 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0142 AC: 2167AN: 152130Hom.: 93 Cov.: 32
GnomAD3 genomes
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2167
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GnomAD3 exomes AF: 0.0271 AC: 6800AN: 250728Hom.: 314 AF XY: 0.0286 AC XY: 3879AN XY: 135560
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GnomAD4 exome AF: 0.0120 AC: 17573AN: 1461820Hom.: 745 Cov.: 33 AF XY: 0.0144 AC XY: 10486AN XY: 727216
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GnomAD4 genome ? AF: 0.0143 AC: 2180AN: 152248Hom.: 96 Cov.: 32 AF XY: 0.0178 AC XY: 1323AN XY: 74432
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ESP6500AA
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ESP6500EA
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32
ExAC
?
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3132
Asia WGS
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227
AN:
3478
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 16, 2019 | This variant is associated with the following publications: (PMID: 29669943) - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Uncertain
D;D;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;.
MutationTaster
Benign
N;N;N;N
PrimateAI
Benign
T
Sift4G
Benign
T;T;T
Polyphen
B;B;.
Vest4
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at