rs17525488

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001256643.1(LTA4H):​c.88-6475delA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0914 in 1,430,700 control chromosomes in the GnomAD database, including 8,003 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.10 ( 1048 hom., cov: 31)
Exomes 𝑓: 0.090 ( 6955 hom. )

Consequence

LTA4H
NM_001256643.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.569
Variant links:
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 -8 ACMG points.

BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LTA4HNM_001256643.1 linkuse as main transcriptc.88-6475delA intron_variant NP_001243572.1 P09960-4
LTA4HNM_001256644.1 linkuse as main transcriptc.88-6475delA intron_variant NP_001243573.1 P09960-3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LTA4HENST00000552789.5 linkuse as main transcriptc.88-6475delA intron_variant 1 ENSP00000449958.1 P09960-4
LTA4HENST00000413268.6 linkuse as main transcriptc.88-6475delA intron_variant 2 ENSP00000395051.2 P09960-3
LTA4HENST00000548852.5 linkuse as main transcriptn.-141delA upstream_gene_variant 2 ENSP00000449340.1 B4DEH5

Frequencies

GnomAD3 genomes
AF:
0.102
AC:
15569
AN:
151894
Hom.:
1042
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0942
Gnomad AMI
AF:
0.0428
Gnomad AMR
AF:
0.0839
Gnomad ASJ
AF:
0.0781
Gnomad EAS
AF:
0.298
Gnomad SAS
AF:
0.219
Gnomad FIN
AF:
0.202
Gnomad MID
AF:
0.0949
Gnomad NFE
AF:
0.0755
Gnomad OTH
AF:
0.0955
GnomAD4 exome
AF:
0.0900
AC:
115143
AN:
1278688
Hom.:
6955
Cov.:
29
AF XY:
0.0927
AC XY:
57307
AN XY:
617976
show subpopulations
Gnomad4 AFR exome
AF:
0.0941
Gnomad4 AMR exome
AF:
0.0762
Gnomad4 ASJ exome
AF:
0.0712
Gnomad4 EAS exome
AF:
0.281
Gnomad4 SAS exome
AF:
0.206
Gnomad4 FIN exome
AF:
0.197
Gnomad4 NFE exome
AF:
0.0721
Gnomad4 OTH exome
AF:
0.101
GnomAD4 genome
AF:
0.103
AC:
15592
AN:
152012
Hom.:
1048
Cov.:
31
AF XY:
0.111
AC XY:
8215
AN XY:
74268
show subpopulations
Gnomad4 AFR
AF:
0.0941
Gnomad4 AMR
AF:
0.0840
Gnomad4 ASJ
AF:
0.0781
Gnomad4 EAS
AF:
0.299
Gnomad4 SAS
AF:
0.219
Gnomad4 FIN
AF:
0.202
Gnomad4 NFE
AF:
0.0755
Gnomad4 OTH
AF:
0.104
Alfa
AF:
0.0838
Hom.:
71
Bravo
AF:
0.0908
Asia WGS
AF:
0.260
AC:
902
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs17525488; hg19: chr12-96429437; API