chr1-67326816-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001374259.2(IL12RB2):c.446G>A(p.Arg149Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00274 in 1,613,810 control chromosomes in the GnomAD database, including 41 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_001374259.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL12RB2 | NM_001374259.2 | c.446G>A | p.Arg149Gln | missense_variant | Exon 5 of 17 | ENST00000674203.2 | NP_001361188.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00816 AC: 1241AN: 152124Hom.: 13 Cov.: 32
GnomAD3 exomes AF: 0.00328 AC: 824AN: 251366Hom.: 6 AF XY: 0.00286 AC XY: 388AN XY: 135866
GnomAD4 exome AF: 0.00217 AC: 3175AN: 1461570Hom.: 28 Cov.: 31 AF XY: 0.00210 AC XY: 1527AN XY: 727096
GnomAD4 genome AF: 0.00819 AC: 1247AN: 152240Hom.: 13 Cov.: 32 AF XY: 0.00781 AC XY: 581AN XY: 74430
ClinVar
Submissions by phenotype
not provided Benign:2
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IL12RB2-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