rs142971951
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The ENST00000324134.11(NLRP12):c.412C>T(p.Arg138Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000527 in 1,614,032 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R138G) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000324134.11 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NLRP12 | NM_144687.4 | c.412C>T | p.Arg138Trp | missense_variant | 3/10 | ENST00000324134.11 | NP_653288.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NLRP12 | ENST00000324134.11 | c.412C>T | p.Arg138Trp | missense_variant | 3/10 | 1 | NM_144687.4 | ENSP00000319377 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000289 AC: 44AN: 152068Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000717 AC: 18AN: 251130Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135836
GnomAD4 exome AF: 0.0000280 AC: 41AN: 1461846Hom.: 0 Cov.: 40 AF XY: 0.0000303 AC XY: 22AN XY: 727224
GnomAD4 genome AF: 0.000289 AC: 44AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74392
ClinVar
Submissions by phenotype
Familial cold autoinflammatory syndrome 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 01, 2023 | - - |
NLRP12-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 18, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at