rs13226149
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_000940.3(PON3):c.63C>T(p.Phe21=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 1,613,292 control chromosomes in the GnomAD database, including 65,269 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.30 ( 7172 hom., cov: 30)
Exomes 𝑓: 0.28 ( 58097 hom. )
Consequence
PON3
NM_000940.3 synonymous
NM_000940.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.77
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 7-95396288-G-A is Benign according to our data. Variant chr7-95396288-G-A is described in ClinVar as [Benign]. Clinvar id is 1268453.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-2.77 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PON3 | NM_000940.3 | c.63C>T | p.Phe21= | synonymous_variant | 1/9 | ENST00000265627.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PON3 | ENST00000265627.10 | c.63C>T | p.Phe21= | synonymous_variant | 1/9 | 1 | NM_000940.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.298 AC: 45165AN: 151612Hom.: 7158 Cov.: 30
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GnomAD3 exomes AF: 0.287 AC: 71408AN: 249158Hom.: 11038 AF XY: 0.293 AC XY: 39504AN XY: 134858
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GnomAD4 exome AF: 0.277 AC: 404529AN: 1461562Hom.: 58097 Cov.: 35 AF XY: 0.280 AC XY: 203898AN XY: 727114
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GnomAD4 genome ? AF: 0.298 AC: 45203AN: 151730Hom.: 7172 Cov.: 30 AF XY: 0.305 AC XY: 22651AN XY: 74152
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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 | Jun 09, 2021 | - - |
Computational 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