1-247418855-G-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PP2PP5_ModerateBS2
The NM_001243133.2(NLRP3):c.55G>C(p.Asp19His) variant causes a missense change. The variant allele was found at a frequency of 0.00000805 in 1,614,084 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Consequence
NM_001243133.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NLRP3 | NM_001243133.2 | c.55G>C | p.Asp19His | missense_variant | Exon 2 of 10 | ENST00000336119.8 | NP_001230062.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NLRP3 | ENST00000336119.8 | c.55G>C | p.Asp19His | missense_variant | Exon 2 of 10 | 1 | NM_001243133.2 | ENSP00000337383.4 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152096Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251292Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135872
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461870Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727238
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74404
ClinVar
Submissions by phenotype
Keratitis fugax hereditaria Pathogenic:2
This variant is interpreted as Likely Pathogenic, for Keratitis fugax hereditaria, autosomal dominant. The following ACMG Tag(s) were applied: PP1-Strong => PP1 upgraded in strength to Strong (https://www.ncbi.nlm.nih.gov/pubmed/29366613). PP3 => Multiple lines of computational evidence support a deleterious effect on the gene or gene product. PM1 => Located in a mutational hot spot and/or critical and well-established functional domain (e.g., active site of an enzyme) without benign variation. PM2-Supporting => PM2 downgraded in strength to Supporting. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at