19-54970118-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_017852.5(NLRP2):c.103C>T(p.Leu35Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000732 in 1,614,098 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_017852.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NLRP2 | NM_017852.5 | c.103C>T | p.Leu35Leu | synonymous_variant | Exon 2 of 13 | ENST00000448584.7 | NP_060322.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000434 AC: 66AN: 152086Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000370 AC: 93AN: 251486Hom.: 0 AF XY: 0.000383 AC XY: 52AN XY: 135920
GnomAD4 exome AF: 0.000763 AC: 1115AN: 1461894Hom.: 1 Cov.: 46 AF XY: 0.000756 AC XY: 550AN XY: 727248
GnomAD4 genome AF: 0.000434 AC: 66AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.000403 AC XY: 30AN XY: 74404
ClinVar
Submissions by phenotype
not provided Benign:2
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NLRP2: BP4, BP7 -
NLRP2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at