chr19-53807553-C-T
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_144687.4(NLRP12):c.2185G>A(p.Gly729Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0001 in 1,614,124 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_144687.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NLRP12 | ENST00000324134.11 | c.2185G>A | p.Gly729Arg | missense_variant | Exon 4 of 10 | 1 | NM_144687.4 | ENSP00000319377.6 | ||
NLRP12 | ENST00000345770.9 | c.2188G>A | p.Gly730Arg | missense_variant | Exon 4 of 9 | 1 | ENSP00000341428.5 | |||
NLRP12 | ENST00000391772.1 | c.2188G>A | p.Gly730Arg | missense_variant | Exon 4 of 7 | 1 | ENSP00000375652.1 |
Frequencies
GnomAD3 genomes AF: 0.000552 AC: 84AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000167 AC: 42AN: 251234Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135828
GnomAD4 exome AF: 0.0000534 AC: 78AN: 1461862Hom.: 0 Cov.: 32 AF XY: 0.0000523 AC XY: 38AN XY: 727232
GnomAD4 genome AF: 0.000552 AC: 84AN: 152262Hom.: 0 Cov.: 32 AF XY: 0.000497 AC XY: 37AN XY: 74454
ClinVar
Submissions by phenotype
Familial cold autoinflammatory syndrome 2 Benign:2
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This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
NLRP12-related disorder Benign:1
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