rs17883013
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000940.3(PON3):c.536C>A(p.Ala179Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00269 in 1,613,816 control chromosomes in the GnomAD database, including 110 homozygotes. In-silico tool predicts 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 -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PON3 | NM_000940.3 | c.536C>A | p.Ala179Asp | missense_variant | 6/9 | ENST00000265627.10 | NP_000931.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PON3 | ENST00000265627.10 | c.536C>A | p.Ala179Asp | missense_variant | 6/9 | 1 | NM_000940.3 | ENSP00000265627.5 |
Frequencies
GnomAD3 genomes AF: 0.0145 AC: 2200AN: 152094Hom.: 54 Cov.: 32
GnomAD3 exomes AF: 0.00380 AC: 953AN: 250852Hom.: 26 AF XY: 0.00256 AC XY: 347AN XY: 135548
GnomAD4 exome AF: 0.00146 AC: 2132AN: 1461604Hom.: 56 Cov.: 31 AF XY: 0.00123 AC XY: 894AN XY: 727100
GnomAD4 genome AF: 0.0145 AC: 2203AN: 152212Hom.: 54 Cov.: 32 AF XY: 0.0137 AC XY: 1020AN XY: 74430
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 10, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at