rs565345523
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6BS1BS2
The NM_002187.3(IL12B):c.506C>T(p.Thr169Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000793 in 1,614,030 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_002187.3 missense
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 |
---|---|---|---|---|---|---|---|
IL12B | NM_002187.3 | c.506C>T | p.Thr169Met | missense_variant | 5/8 | ENST00000231228.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL12B | ENST00000231228.3 | c.506C>T | p.Thr169Met | missense_variant | 5/8 | 1 | NM_002187.3 | P1 | |
IL12B | ENST00000696750.1 | c.-125C>T | 5_prime_UTR_variant | 2/5 | |||||
IL12B | ENST00000696751.1 | c.*1C>T | 3_prime_UTR_variant, NMD_transcript_variant | 4/7 | |||||
ENST00000521472.6 | n.290-5037G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000163 AC: 41AN: 251124Hom.: 1 AF XY: 0.000236 AC XY: 32AN XY: 135730
GnomAD4 exome AF: 0.0000800 AC: 117AN: 1461732Hom.: 5 Cov.: 32 AF XY: 0.000120 AC XY: 87AN XY: 727184
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152298Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74476
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 | Nov 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at