rs10514611
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002163.4(IRF8):c.*354C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 279,678 control chromosomes in the GnomAD database, including 6,989 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.23 ( 3935 hom., cov: 33)
Exomes 𝑓: 0.21 ( 3054 hom. )
Consequence
IRF8
NM_002163.4 3_prime_UTR
NM_002163.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.506
Genes affected
IRF8 (HGNC:5358): (interferon regulatory factor 8) Interferon consensus sequence-binding protein (ICSBP) is a transcription factor of the interferon (IFN) regulatory factor (IRF) family. Proteins of this family are composed of a conserved DNA-binding domain in the N-terminal region and a divergent C-terminal region that serves as the regulatory domain. The IRF family proteins bind to the IFN-stimulated response element (ISRE) and regulate expression of genes stimulated by type I IFNs, namely IFN-alpha and IFN-beta. IRF family proteins also control expression of IFN-alpha and IFN-beta-regulated genes that are induced by viral infection. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 16-85921636-C-T is Benign according to our data. Variant chr16-85921636-C-T is described in ClinVar as [Benign]. Clinvar id is 1168174.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IRF8 | NM_002163.4 | c.*354C>T | 3_prime_UTR_variant | 9/9 | ENST00000268638.10 | ||
IRF8 | NM_001363907.1 | c.*354C>T | 3_prime_UTR_variant | 9/9 | |||
IRF8 | NM_001363908.1 | c.*354C>T | 3_prime_UTR_variant | 7/7 | |||
IRF8 | XM_047434052.1 | c.*354C>T | 3_prime_UTR_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRF8 | ENST00000268638.10 | c.*354C>T | 3_prime_UTR_variant | 9/9 | 1 | NM_002163.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.225 AC: 34230AN: 152012Hom.: 3929 Cov.: 33
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GnomAD4 exome AF: 0.212 AC: 27001AN: 127548Hom.: 3054 Cov.: 0 AF XY: 0.205 AC XY: 13747AN XY: 67134
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GnomAD4 genome ? AF: 0.225 AC: 34268AN: 152130Hom.: 3935 Cov.: 33 AF XY: 0.226 AC XY: 16770AN XY: 74366
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Mendelian susceptibility to mycobacterial diseases due to partial IRF8 deficiency;C4016741:Immunodeficiency 32B Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at