19-53794055-G-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_144687.4(NLRP12):c.3180C>G(p.Gly1060=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000664 in 1,611,894 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. G1060G) has been classified as Likely benign.
Frequency
Consequence
NM_144687.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NLRP12 | NM_144687.4 | c.3180C>G | p.Gly1060= | synonymous_variant | 10/10 | ENST00000324134.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NLRP12 | ENST00000324134.11 | c.3180C>G | p.Gly1060= | synonymous_variant | 10/10 | 1 | NM_144687.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152100Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000115 AC: 29AN: 251486Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135922
GnomAD4 exome AF: 0.0000685 AC: 100AN: 1459794Hom.: 0 Cov.: 30 AF XY: 0.0000537 AC XY: 39AN XY: 726388
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152100Hom.: 0 Cov.: 31 AF XY: 0.0000538 AC XY: 4AN XY: 74314
ClinVar
Submissions by phenotype
Familial cold autoinflammatory syndrome 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at