rs13306698
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000446.7(PON1):āc.478A>Gā(p.Arg160Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00234 in 1,614,108 control chromosomes in the GnomAD database, including 131 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000446.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PON1 | NM_000446.7 | c.478A>G | p.Arg160Gly | missense_variant | 5/9 | ENST00000222381.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PON1 | ENST00000222381.8 | c.478A>G | p.Arg160Gly | missense_variant | 5/9 | 1 | NM_000446.7 | P1 | |
PON1 | ENST00000433729.1 | c.*203A>G | 3_prime_UTR_variant, NMD_transcript_variant | 5/9 | 3 | ||||
PON1 | ENST00000470502.1 | downstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00293 AC: 446AN: 152210Hom.: 22 Cov.: 32
GnomAD3 exomes AF: 0.00598 AC: 1502AN: 251310Hom.: 48 AF XY: 0.00562 AC XY: 764AN XY: 135834
GnomAD4 exome AF: 0.00227 AC: 3325AN: 1461780Hom.: 109 Cov.: 31 AF XY: 0.00228 AC XY: 1659AN XY: 727210
GnomAD4 genome ? AF: 0.00291 AC: 444AN: 152328Hom.: 22 Cov.: 32 AF XY: 0.00350 AC XY: 261AN XY: 74490
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2021 | This variant is associated with the following publications: (PMID: 12588779) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at