chr19-55954767-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_176811.2(NLRP8):c.709C>T(p.Arg237Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00255 in 1,614,178 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R237H) has been classified as Uncertain significance.
Frequency
Consequence
NM_176811.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NLRP8 | NM_176811.2 | c.709C>T | p.Arg237Cys | missense_variant | 3/10 | ENST00000291971.7 | |
NLRP8 | NM_001317000.1 | c.709C>T | p.Arg237Cys | missense_variant | 3/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NLRP8 | ENST00000291971.7 | c.709C>T | p.Arg237Cys | missense_variant | 3/10 | 1 | NM_176811.2 | P2 | |
NLRP8 | ENST00000590542.1 | c.709C>T | p.Arg237Cys | missense_variant | 3/10 | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00164 AC: 249AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00137 AC: 344AN: 251320Hom.: 0 AF XY: 0.00133 AC XY: 181AN XY: 135820
GnomAD4 exome AF: 0.00265 AC: 3872AN: 1461884Hom.: 11 Cov.: 31 AF XY: 0.00257 AC XY: 1872AN XY: 727242
GnomAD4 genome ? AF: 0.00163 AC: 249AN: 152294Hom.: 0 Cov.: 32 AF XY: 0.00138 AC XY: 103AN XY: 74474
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 17, 2023 | The c.709C>T (p.R237C) alteration is located in exon 3 (coding exon 3) of the NLRP8 gene. This alteration results from a C to T substitution at nucleotide position 709, causing the arginine (R) at amino acid position 237 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at