rs202106699
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1
The NM_005535.3(IL12RB1):c.1960G>A(p.Asp654Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00065 in 1,586,708 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_005535.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL12RB1 | NM_005535.3 | c.1960G>A | p.Asp654Asn | missense_variant | 16/17 | ENST00000593993.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL12RB1 | ENST00000593993.7 | c.1960G>A | p.Asp654Asn | missense_variant | 16/17 | 1 | NM_005535.3 | P1 | |
IL12RB1 | ENST00000600835.6 | c.1960G>A | p.Asp654Asn | missense_variant | 17/18 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000421 AC: 64AN: 152012Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000568 AC: 119AN: 209450Hom.: 0 AF XY: 0.000549 AC XY: 62AN XY: 113018
GnomAD4 exome AF: 0.000674 AC: 967AN: 1434578Hom.: 0 Cov.: 31 AF XY: 0.000603 AC XY: 429AN XY: 711438
GnomAD4 genome ? AF: 0.000421 AC: 64AN: 152130Hom.: 0 Cov.: 32 AF XY: 0.000363 AC XY: 27AN XY: 74382
ClinVar
Submissions by phenotype
Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 05, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at