rs17878827
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000940.3(PON3):c.436G>A(p.Glu146Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000815 in 1,613,104 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000940.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PON3 | NM_000940.3 | c.436G>A | p.Glu146Lys | missense_variant | 5/9 | ENST00000265627.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PON3 | ENST00000265627.10 | c.436G>A | p.Glu146Lys | missense_variant | 5/9 | 1 | NM_000940.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00357 AC: 543AN: 152092Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.00114 AC: 286AN: 250976Hom.: 2 AF XY: 0.000922 AC XY: 125AN XY: 135620
GnomAD4 exome AF: 0.000523 AC: 764AN: 1460894Hom.: 4 Cov.: 31 AF XY: 0.000491 AC XY: 357AN XY: 726806
GnomAD4 genome ? AF: 0.00361 AC: 550AN: 152210Hom.: 4 Cov.: 33 AF XY: 0.00357 AC XY: 266AN XY: 74420
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at