chr12-96013217-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_000895.3(LTA4H):c.1350C>T(p.Tyr450=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00171 in 1,613,678 control chromosomes in the GnomAD database, including 47 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0092 ( 23 hom., cov: 32)
Exomes 𝑓: 0.00093 ( 24 hom. )
Consequence
LTA4H
NM_000895.3 synonymous
NM_000895.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.10
Genes affected
LTA4H (HGNC:6710): (leukotriene A4 hydrolase) The protein encoded by this gene is an enzyme that contains both hydrolase and aminopeptidase activities. The hydrolase activity is used in the final step of the biosynthesis of leukotriene B4, a proinflammatory mediator. The aminopeptidase activity has been shown to degrade proline-glycine-proline (PGP), a neutrophil chemoattractant and biomarker for chronic obstructive pulmonary disease (COPD). Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
?
Variant 12-96013217-G-A is Benign according to our data. Variant chr12-96013217-G-A is described in ClinVar as [Benign]. Clinvar id is 786610.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.1 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00922 (1404/152218) while in subpopulation AFR AF= 0.0323 (1340/41516). AF 95% confidence interval is 0.0308. There are 23 homozygotes in gnomad4. There are 691 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 22 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LTA4H | NM_000895.3 | c.1350C>T | p.Tyr450= | synonymous_variant | 14/19 | ENST00000228740.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LTA4H | ENST00000228740.7 | c.1350C>T | p.Tyr450= | synonymous_variant | 14/19 | 1 | NM_000895.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00923 AC: 1404AN: 152100Hom.: 22 Cov.: 32
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GnomAD3 exomes AF: 0.00229 AC: 576AN: 251238Hom.: 8 AF XY: 0.00167 AC XY: 227AN XY: 135782
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GnomAD4 exome AF: 0.000929 AC: 1357AN: 1461460Hom.: 24 Cov.: 29 AF XY: 0.000796 AC XY: 579AN XY: 727056
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GnomAD4 genome ? AF: 0.00922 AC: 1404AN: 152218Hom.: 23 Cov.: 32 AF XY: 0.00928 AC XY: 691AN XY: 74446
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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 | Invitae | Dec 31, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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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