NM_144687.4:c.2469C>T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_144687.4(NLRP12):c.2469C>T(p.Leu823Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 1,613,480 control chromosomes in the GnomAD database, including 253,416 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. L823L) has been classified as Benign.
Frequency
Consequence
NM_144687.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NLRP12 | ENST00000324134.11 | c.2469C>T | p.Leu823Leu | synonymous_variant | Exon 6 of 10 | 1 | NM_144687.4 | ENSP00000319377.6 | ||
NLRP12 | ENST00000345770.9 | c.2472C>T | p.Leu824Leu | synonymous_variant | Exon 6 of 9 | 1 | ENSP00000341428.5 | |||
NLRP12 | ENST00000391772.1 | c.2472C>T | p.Leu824Leu | synonymous_variant | Exon 6 of 7 | 1 | ENSP00000375652.1 |
Frequencies
GnomAD3 genomes AF: 0.466 AC: 70669AN: 151808Hom.: 18602 Cov.: 31
GnomAD3 exomes AF: 0.530 AC: 133138AN: 251008Hom.: 36924 AF XY: 0.531 AC XY: 72112AN XY: 135714
GnomAD4 exome AF: 0.561 AC: 820227AN: 1461552Hom.: 234809 Cov.: 48 AF XY: 0.558 AC XY: 405557AN XY: 727106
GnomAD4 genome AF: 0.465 AC: 70680AN: 151928Hom.: 18607 Cov.: 31 AF XY: 0.469 AC XY: 34777AN XY: 74228
ClinVar
Submissions by phenotype
not specified Benign:3
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
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This variant is classified as Benign based on local population frequency. This variant was detected in 81% of patients studied by a panel of primary immunodeficiencies. Number of patients: 78. Only high quality variants are reported. -
Familial cold autoinflammatory syndrome 2 Benign:3
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not provided Benign:1
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Familial cold autoinflammatory syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at