chr2-32224599-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001199138.2(NLRC4):c.2949A>C(p.Leu983Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001199138.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NLRC4 | NM_001199138.2 | c.2949A>C | p.Leu983Phe | missense_variant | 9/9 | ENST00000402280.6 | |
NLRC4 | NM_001199139.1 | c.2949A>C | p.Leu983Phe | missense_variant | 9/9 | ||
NLRC4 | NM_021209.4 | c.2949A>C | p.Leu983Phe | missense_variant | 9/9 | ||
NLRC4 | NM_001302504.1 | c.954A>C | p.Leu318Phe | missense_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NLRC4 | ENST00000402280.6 | c.2949A>C | p.Leu983Phe | missense_variant | 9/9 | 1 | NM_001199138.2 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
NLRC4-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 31, 2024 | The NLRC4 c.2949A>C variant is predicted to result in the amino acid substitution p.Leu983Phe. To our knowledge, this variant has not been reported in the literature or in a large population database, indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.