19-18059905-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005535.3(IL12RB1):c.1972T>C(p.Cys658Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000035 in 1,426,536 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005535.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL12RB1 | NM_005535.3 | c.1972T>C | p.Cys658Arg | missense_variant | 16/17 | ENST00000593993.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL12RB1 | ENST00000593993.7 | c.1972T>C | p.Cys658Arg | missense_variant | 16/17 | 1 | NM_005535.3 | P1 | |
IL12RB1 | ENST00000600835.6 | c.1972T>C | p.Cys658Arg | missense_variant | 17/18 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 1AN: 147654Hom.: 0 Cov.: 31 FAILED QC
GnomAD3 exomes AF: 0.0000149 AC: 3AN: 201030Hom.: 0 AF XY: 0.0000185 AC XY: 2AN XY: 108322
GnomAD4 exome AF: 0.00000350 AC: 5AN: 1426536Hom.: 0 Cov.: 31 AF XY: 0.00000566 AC XY: 4AN XY: 707012
GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.00000677 AC: 1AN: 147758Hom.: 0 Cov.: 31 AF XY: 0.0000139 AC XY: 1AN XY: 72048
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 11, 2022 | The c.1972T>C (p.C658R) alteration is located in exon 16 (coding exon 16) of the IL12RB1 gene. This alteration results from a T to C substitution at nucleotide position 1972, causing the cysteine (C) at amino acid position 658 to be replaced by an arginine (R). 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