rs147057451
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_002163.4(IRF8):c.1275C>G(p.Thr425=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,350 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T425T) has been classified as Benign.
Frequency
Consequence
NM_002163.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IRF8 | NM_002163.4 | c.1275C>G | p.Thr425= | synonymous_variant | 9/9 | ENST00000268638.10 | |
IRF8 | NM_001363907.1 | c.1305C>G | p.Thr435= | synonymous_variant | 9/9 | ||
IRF8 | NM_001363908.1 | c.663C>G | p.Thr221= | synonymous_variant | 7/7 | ||
IRF8 | XM_047434052.1 | c.1305C>G | p.Thr435= | synonymous_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRF8 | ENST00000268638.10 | c.1275C>G | p.Thr425= | synonymous_variant | 9/9 | 1 | NM_002163.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251012Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135722
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461350Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727010
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Mendelian susceptibility to mycobacterial diseases due to partial IRF8 deficiency;C4016741:Immunodeficiency 32B Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 16, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at