rs10954213
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001098629.3(IRF5):c.*555G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 152,430 control chromosomes in the GnomAD database, including 25,782 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).
Frequency
Genomes: 𝑓 0.58 ( 25754 hom., cov: 34)
Exomes 𝑓: 0.50 ( 28 hom. )
Consequence
IRF5
NM_001098629.3 3_prime_UTR
NM_001098629.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.53
Genes affected
IRF5 (HGNC:6120): (interferon regulatory factor 5) This gene encodes a member of the interferon regulatory factor (IRF) family, a group of transcription factors with diverse roles, including virus-mediated activation of interferon, and modulation of cell growth, differentiation, apoptosis, and immune system activity. Members of the IRF family are characterized by a conserved N-terminal DNA-binding domain containing tryptophan (W) repeats. Alternative promoter use and alternative splicing result in multiple transcript variants, and a 30-nt indel polymorphism (SNP rs60344245) can result in loss of a 10-aa segment. [provided by RefSeq, Dec 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IRF5 | NM_001098629.3 | c.*555G>A | 3_prime_UTR_variant | 9/9 | ENST00000357234.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRF5 | ENST00000357234.10 | c.*555G>A | 3_prime_UTR_variant | 9/9 | 1 | NM_001098629.3 |
Frequencies
GnomAD3 genomes AF: 0.579 AC: 87999AN: 152102Hom.: 25745 Cov.: 34
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GnomAD4 exome AF: 0.500 AC: 105AN: 210Hom.: 28 Cov.: 0 AF XY: 0.510 AC XY: 52AN XY: 102
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GnomAD4 genome AF: 0.578 AC: 88047AN: 152220Hom.: 25754 Cov.: 34 AF XY: 0.576 AC XY: 42895AN XY: 74414
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ClinVar
Significance: risk factor
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Systemic lupus erythematosus, susceptibility to, 10 Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Mar 15, 2008 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at