rs2004640
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001098629(IRF5):c.-12+198T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 151418 control chromosomes in the gnomAD Genomes database, including 21275 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 0.53 ( 21275 hom., cov: 32)
Consequence
IRF5
NM_001098629 intron
NM_001098629 intron
Scores
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.802
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IRF5 | NM_001098629.3 | c.-12+198T>G | intron_variant | ENST00000357234.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRF5 | ENST00000357234.10 | c.-12+198T>G | intron_variant | 1 | NM_001098629.3 |
Frequencies
GnomAD3 genomes AF: 0.526 AC: 79628AN: 151418Hom.: 21275 Cov.: 32
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GnomAD4 exome AF: 0.559 AC: 113AN: 202Hom.: 37 AF XY: 0.549 AC XY: 89AN XY: 162
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Splicing
Find out SpliceAI and Pangolin per-transcript scores at