rs147057451
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_002163.4(IRF8):āc.1275C>Gā(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 (ā ). 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