rs9282763
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002198.3(IRF1):c.545-68A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 1,608,276 control chromosomes in the GnomAD database, including 97,197 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.38 ( 11331 hom., cov: 33)
Exomes 𝑓: 0.34 ( 85866 hom. )
Consequence
IRF1
NM_002198.3 intron
NM_002198.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.32
Genes affected
IRF1 (HGNC:6116): (interferon regulatory factor 1) The protein encoded by this gene is a transcriptional regulator and tumor suppressor, serving as an activator of genes involved in both innate and acquired immune responses. The encoded protein activates the transcription of genes involved in the body's response to viruses and bacteria, playing a role in cell proliferation, apoptosis, the immune response, and DNA damage response. This protein represses the transcription of several other genes. As a tumor suppressor, it both suppresses tumor cell growth and stimulates an immune response against tumor cells. Defects in this gene have been associated with gastric cancer, myelogenous leukemia, and lung cancer. [provided by RefSeq, Aug 2017]
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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=-0.88).
BP6
?
Variant 5-132486441-T-C is Benign according to our data. Variant chr5-132486441-T-C is described in ClinVar as [Benign]. Clinvar id is 2688382.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IRF1 | NM_002198.3 | c.545-68A>G | intron_variant | ENST00000245414.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRF1 | ENST00000245414.9 | c.545-68A>G | intron_variant | 1 | NM_002198.3 | P1 | |||
IRF1-AS1 | ENST00000612967.2 | n.530T>C | non_coding_transcript_exon_variant | 4/4 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.379 AC: 57648AN: 152030Hom.: 11317 Cov.: 33
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GnomAD3 exomes AF: 0.347 AC: 85735AN: 246886Hom.: 14978 AF XY: 0.347 AC XY: 46390AN XY: 133812
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GnomAD4 exome AF: 0.341 AC: 496764AN: 1456128Hom.: 85866 Cov.: 34 AF XY: 0.342 AC XY: 247669AN XY: 724490
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GnomAD4 genome ? AF: 0.379 AC: 57705AN: 152148Hom.: 11331 Cov.: 33 AF XY: 0.378 AC XY: 28154AN XY: 74388
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 66% of patients studied by a panel of primary immunodeficiencies. Number of patients: 58. Only high quality variants are reported. - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at