19-55902194-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_176810.2(NLRP13):c.2630G>A(p.Cys877Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,514 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_176810.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NLRP13 | ENST00000342929.4 | c.2630G>A | p.Cys877Tyr | missense_variant | Exon 9 of 11 | 1 | NM_176810.2 | ENSP00000343891.3 | ||
NLRP13 | ENST00000588751.5 | c.2630G>A | p.Cys877Tyr | missense_variant | Exon 9 of 12 | 5 | ENSP00000467899.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461514Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727064
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2630G>A (p.C877Y) alteration is located in exon 9 (coding exon 9) of the NLRP13 gene. This alteration results from a G to A substitution at nucleotide position 2630, causing the cysteine (C) at amino acid position 877 to be replaced by a tyrosine (Y). 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