rs3917564
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000446.7(PON1):c.781-67T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0139 in 1,457,726 control chromosomes in the GnomAD database, including 879 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 0.047 ( 453 hom., cov: 32)
Exomes 𝑓: 0.010 ( 426 hom. )
Consequence
PON1
NM_000446.7 intron
NM_000446.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.294
Genes affected
PON1 (HGNC:9204): (paraoxonase 1) This gene encodes a member of the paraoxonase family of enzymes and exhibits lactonase and ester hydrolase activity. Following synthesis in the kidney and liver, the enzyme is secreted into the circulation, where it binds to high density lipoprotein (HDL) particles and hydrolyzes thiolactones and xenobiotics, including paraoxon, a metabolite of the insecticide parathion. Polymorphisms in this gene may be associated with coronary artery disease and diabetic retinopathy. The gene is found in a cluster of three related paraoxonase genes on chromosome 7. [provided by RefSeq, Aug 2017]
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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=-0.81).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PON1 | NM_000446.7 | c.781-67T>C | intron_variant | ENST00000222381.8 | NP_000437.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PON1 | ENST00000222381.8 | c.781-67T>C | intron_variant | 1 | NM_000446.7 | ENSP00000222381.3 | ||||
PON1 | ENST00000462594.1 | n.4T>C | non_coding_transcript_exon_variant | 1/2 | 2 | |||||
PON1 | ENST00000433729.1 | n.*506-67T>C | intron_variant | 3 | ENSP00000407359.1 |
Frequencies
GnomAD3 genomes AF: 0.0467 AC: 7099AN: 152104Hom.: 447 Cov.: 32
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GnomAD4 exome AF: 0.0101 AC: 13147AN: 1305504Hom.: 426 Cov.: 19 AF XY: 0.00952 AC XY: 6247AN XY: 656334
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GnomAD4 genome AF: 0.0468 AC: 7131AN: 152222Hom.: 453 Cov.: 32 AF XY: 0.0449 AC XY: 3342AN XY: 74428
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at