chr1-247436088-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 1P and 13B. PP2BP4_StrongBP6BS1BS2
The NM_001243133.2(NLRP3):c.2611G>A(p.Ala871Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000328 in 1,614,092 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001243133.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NLRP3 | NM_001243133.2 | c.2611G>A | p.Ala871Thr | missense_variant | 7/10 | ENST00000336119.8 | NP_001230062.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NLRP3 | ENST00000336119.8 | c.2611G>A | p.Ala871Thr | missense_variant | 7/10 | 1 | NM_001243133.2 | ENSP00000337383.4 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152098Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251470Hom.: 0 AF XY: 0.0000441 AC XY: 6AN XY: 135910
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461878Hom.: 0 Cov.: 33 AF XY: 0.0000179 AC XY: 13AN XY: 727240
GnomAD4 genome AF: 0.000164 AC: 25AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74438
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Aug 05, 2013 | To our knowledge, the A873T missense substitution has neither been published as a mutation, nor as a benign polymorphism. A873T represents a semi-conservative substitution between two uncharged amino acids as a non-polar Alanine residue is replaced with a polar Threonine residue at a position that is not well conserved. The NHLBI ESP Exome Variant Server reports that A873T was not observed at any significant frequency in individuals of African American or European backgrounds, indicating it is not a common benign variant in these populations. Therefore, the clinical significance of A873T is unclear at this time - |
Cryopyrin associated periodic syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 22, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at