7-95365242-T-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000940.3(PON3):c.495-1179A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 152,116 control chromosomes in the GnomAD database, including 15,819 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.44 ( 15807 hom., cov: 32)
Exomes 𝑓: 0.40 ( 12 hom. )
Consequence
PON3
NM_000940.3 intron
NM_000940.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.49
Genes affected
PON3 (HGNC:9206): (paraoxonase 3) This gene is a member of the paraoxonase family and lies in a cluster on chromosome 7 with the other two family members. The encoded protein is secreted into the bloodstream and associates with high-density lipoprotein (HDL). The protein also rapidly hydrolyzes lactones and can inhibit the oxidation of low-density lipoprotein (LDL), a function that is believed to slow the initiation and progression of atherosclerosis. Alternatively spliced variants which encode different protein isoforms have been described; however, only one has been fully characterized. [provided by RefSeq, Jul 2008]
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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=-0.86).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PON3 | NM_000940.3 | c.495-1179A>G | intron_variant | ENST00000265627.10 | NP_000931.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PON3 | ENST00000265627.10 | c.495-1179A>G | intron_variant | 1 | NM_000940.3 | ENSP00000265627.5 |
Frequencies
GnomAD3 genomes AF: 0.441 AC: 66961AN: 151908Hom.: 15800 Cov.: 32
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GnomAD4 exome AF: 0.400 AC: 36AN: 90Hom.: 12 Cov.: 0 AF XY: 0.482 AC XY: 27AN XY: 56
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GnomAD4 genome AF: 0.441 AC: 66989AN: 152026Hom.: 15807 Cov.: 32 AF XY: 0.455 AC XY: 33824AN XY: 74298
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ClinVar
Not reported inComputational scores
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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
Find out detailed SpliceAI scores and Pangolin per-transcript scores at