19-56003968-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_153447.4(NLRP5):c.315C>T(p.Asn105Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 1,613,728 control chromosomes in the GnomAD database, including 16,254 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_153447.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NLRP5 | ENST00000390649.8 | c.315C>T | p.Asn105Asn | synonymous_variant | Exon 2 of 15 | 1 | NM_153447.4 | ENSP00000375063.3 | ||
NLRP5 | ENST00000597673.1 | n.234C>T | non_coding_transcript_exon_variant | Exon 1 of 5 | 5 | ENSP00000471494.1 |
Frequencies
GnomAD3 genomes AF: 0.155 AC: 23596AN: 151966Hom.: 2101 Cov.: 32
GnomAD3 exomes AF: 0.166 AC: 41265AN: 249166Hom.: 4261 AF XY: 0.157 AC XY: 21200AN XY: 135194
GnomAD4 exome AF: 0.129 AC: 187864AN: 1461644Hom.: 14148 Cov.: 33 AF XY: 0.127 AC XY: 92410AN XY: 727104
GnomAD4 genome AF: 0.155 AC: 23621AN: 152084Hom.: 2106 Cov.: 32 AF XY: 0.160 AC XY: 11891AN XY: 74344
ClinVar
Submissions by phenotype
NLRP5-related disorder Benign:1
This variant is classified as 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