rs10954214
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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.*761C>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 0.636 in 151,924 control chromosomes in the GnomAD database, including 31,083 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.64 ( 31076 hom., cov: 31)
Exomes 𝑓: 0.66 ( 7 hom. )
Consequence
IRF5
NM_001098629.3 3_prime_UTR
NM_001098629.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.665
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=-0.48).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IRF5 | NM_001098629.3 | c.*761C>T | 3_prime_UTR_variant | 9/9 | ENST00000357234.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRF5 | ENST00000357234.10 | c.*761C>T | 3_prime_UTR_variant | 9/9 | 1 | NM_001098629.3 |
Frequencies
GnomAD3 genomes ? AF: 0.636 AC: 96577AN: 151774Hom.: 31050 Cov.: 31
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GnomAD4 exome AF: 0.656 AC: 21AN: 32Hom.: 7 Cov.: 0 AF XY: 0.750 AC XY: 9AN XY: 12
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GnomAD4 genome ? AF: 0.636 AC: 96647AN: 151892Hom.: 31076 Cov.: 31 AF XY: 0.637 AC XY: 47302AN XY: 74214
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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