rs10045130
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_002187.3(IL12B):c.544G>A(p.Gly182Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000269 in 1,614,182 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_002187.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL12B | NM_002187.3 | c.544G>A | p.Gly182Arg | missense_variant | 5/8 | ENST00000231228.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL12B | ENST00000231228.3 | c.544G>A | p.Gly182Arg | missense_variant | 5/8 | 1 | NM_002187.3 | P1 | |
IL12B | ENST00000696750.1 | c.-87G>A | 5_prime_UTR_variant | 2/5 | |||||
IL12B | ENST00000696751.1 | c.*39G>A | 3_prime_UTR_variant, NMD_transcript_variant | 4/7 | |||||
ENST00000521472.6 | n.290-5075C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00156 AC: 237AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000362 AC: 91AN: 251200Hom.: 0 AF XY: 0.000273 AC XY: 37AN XY: 135748
GnomAD4 exome AF: 0.000135 AC: 197AN: 1461852Hom.: 0 Cov.: 32 AF XY: 0.000114 AC XY: 83AN XY: 727236
GnomAD4 genome ? AF: 0.00156 AC: 238AN: 152330Hom.: 0 Cov.: 32 AF XY: 0.00158 AC XY: 118AN XY: 74492
ClinVar
Submissions by phenotype
Mendelian susceptibility to mycobacterial diseases due to complete IL12B deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 20, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at