11-612604-TGGGCTGCTCCAGCTTTCTGGAGTTCTCATTAGACTGGGTTCTAGGC-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP7
The NM_001572.5(IRF7):c.1507_*40del variant causes a stop retained, 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000933 in 1,607,554 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000089 ( 0 hom. )
Consequence
IRF7
NM_001572.5 stop_retained, 3_prime_UTR
NM_001572.5 stop_retained, 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.495
Genes affected
IRF7 (HGNC:6122): (interferon regulatory factor 7) This gene encodes interferon regulatory factor 7, a member of the interferon regulatory transcription factor (IRF) family. It has been shown to play a role in the transcriptional activation of virus-inducible cellular genes, including interferon beta chain genes. Inducible expression of IRF7 is largely restricted to lymphoid tissue. The encoded protein plays an important role in the innate immune response against DNA and RNA viruses. [provided by RefSeq, Jul 2021]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP7
?
Synonymous conserved (PhyloP=0.495 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IRF7 | NM_001572.5 | c.1507_*40del | stop_retained_variant, 3_prime_UTR_variant | 11/11 | ENST00000525445.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRF7 | ENST00000525445.6 | c.1507_*40del | stop_retained_variant, 3_prime_UTR_variant | 11/11 | 5 | NM_001572.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152156Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000162 AC: 4AN: 247130Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134362
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GnomAD4 exome AF: 0.00000893 AC: 13AN: 1455398Hom.: 0 AF XY: 0.0000111 AC XY: 8AN XY: 723668
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Immunodeficiency 39 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 27, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals affected with IRF7-related conditions. This variant is present in population databases (rs772699762, gnomAD 0.02%). This sequence change disrupts the translational stop signal of the IRF7 mRNA. It is expected to extend the length of the IRF7 protein by 0 additional amino acid residues. - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at