7-95298612-C-T
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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.*332G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 385,974 control chromosomes in the GnomAD database, including 96,441 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 0.65 ( 33094 hom., cov: 31)
Exomes 𝑓: 0.73 ( 63347 hom. )
Consequence
PON1
NM_000446.7 3_prime_UTR
NM_000446.7 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.180
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=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.751 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PON1 | NM_000446.7 | c.*332G>A | 3_prime_UTR_variant | 9/9 | ENST00000222381.8 | NP_000437.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PON1 | ENST00000222381.8 | c.*332G>A | 3_prime_UTR_variant | 9/9 | 1 | NM_000446.7 | ENSP00000222381 | P1 |
Frequencies
GnomAD3 genomes AF: 0.646 AC: 98112AN: 151862Hom.: 33099 Cov.: 31
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GnomAD4 exome AF: 0.732 AC: 171203AN: 233994Hom.: 63347 Cov.: 2 AF XY: 0.737 AC XY: 93577AN XY: 126966
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GnomAD4 genome AF: 0.646 AC: 98133AN: 151980Hom.: 33094 Cov.: 31 AF XY: 0.647 AC XY: 48075AN XY: 74274
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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