1-165632229-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004528.4(MGST3):c.-8+936G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 1,610,452 control chromosomes in the GnomAD database, including 318,698 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).
Frequency
Genomes: 𝑓 0.58 ( 26822 hom., cov: 32)
Exomes 𝑓: 0.63 ( 291876 hom. )
Consequence
MGST3
NM_004528.4 intron
NM_004528.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.147
Genes affected
MGST3 (HGNC:7064): (microsomal glutathione S-transferase 3) This gene encodes a member of the MAPEG (Membrane Associated Proteins in Eicosanoid and Glutathione metabolism) protein family. Members of this family are involved in the production of leukotrienes and prostaglandin E, important mediators of inflammation. This gene encodes an enzyme which catalyzes the conjugation of leukotriene A4 and reduced glutathione to produce leukotriene C4. This enzyme also demonstrates glutathione-dependent peroxidase activity towards lipid hydroperoxides.[provided by RefSeq, May 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MGST3 | NM_004528.4 | c.-8+936G>A | intron_variant | ENST00000367889.8 | |||
MGST3 | XM_047421030.1 | c.-9-2G>A | splice_acceptor_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MGST3 | ENST00000367889.8 | c.-8+936G>A | intron_variant | 1 | NM_004528.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.577 AC: 87662AN: 151994Hom.: 26802 Cov.: 32
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GnomAD3 exomes AF: 0.673 AC: 162575AN: 241404Hom.: 56869 AF XY: 0.677 AC XY: 89677AN XY: 132560
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GnomAD4 exome AF: 0.626 AC: 913255AN: 1458340Hom.: 291876 Cov.: 36 AF XY: 0.632 AC XY: 458347AN XY: 725536
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GnomAD4 genome ? AF: 0.577 AC: 87711AN: 152112Hom.: 26822 Cov.: 32 AF XY: 0.586 AC XY: 43540AN XY: 74362
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ClinVar
Significance: association
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Pulmonary disease, chronic obstructive, susceptibility to Other:1
association, no assertion criteria provided | research | HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas | Jul 05, 2022 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: 45
Find out detailed SpliceAI scores and Pangolin per-transcript scores at