rs1979522
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001366544.2(IRAG2):c.606+762C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0876 in 413,390 control chromosomes in the GnomAD database, including 1,790 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 0.082 ( 535 hom., cov: 32)
Exomes 𝑓: 0.091 ( 1255 hom. )
Consequence
IRAG2
NM_001366544.2 intron
NM_001366544.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.140
Genes affected
IRAG2 (HGNC:6690): (inositol 1,4,5-triphosphate receptor associated 2) The protein encode dby this gene is expressed in a developmentally regulated manner in lymphoid cell lines and tissues. The protein is localized to the cytoplasmic face of the endoplasmic reticulum. [provided by RefSeq, Jul 2008]
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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=-0.83).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IRAG2 | NM_001366544.2 | c.606+762C>T | intron_variant | ENST00000556887.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRAG2 | ENST00000556887.6 | c.606+762C>T | intron_variant | 5 | NM_001366544.2 |
Frequencies
GnomAD3 genomes ? AF: 0.0824 AC: 12521AN: 152002Hom.: 532 Cov.: 32
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GnomAD4 exome AF: 0.0907 AC: 23686AN: 261272Hom.: 1255 Cov.: 0 AF XY: 0.0948 AC XY: 14037AN XY: 148112
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GnomAD4 genome ? AF: 0.0824 AC: 12533AN: 152118Hom.: 535 Cov.: 32 AF XY: 0.0796 AC XY: 5922AN XY: 74372
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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