rs11042902
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PVS1_ModerateBA1
The ENST00000534266.6(IRAG1):c.-670-2G>A variant causes a splice acceptor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 1,585,126 control chromosomes in the GnomAD database, including 66,537 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
ENST00000534266.6 splice_acceptor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IRAG1 | ENST00000423302.7 | c.226-5G>A | splice_region_variant, intron_variant | Intron 2 of 20 | 2 | NM_130385.4 | ENSP00000412130.2 | |||
IRAG1 | ENST00000534266.6 | c.-670-2G>A | splice_acceptor_variant, intron_variant | Intron 1 of 18 | 2 | ENSP00000433296.2 | ||||
IRAG1 | ENST00000526414.5 | n.70-2G>A | splice_acceptor_variant, intron_variant | Intron 2 of 16 | 2 | ENSP00000435658.1 |
Frequencies
GnomAD3 genomes AF: 0.254 AC: 38581AN: 151808Hom.: 5380 Cov.: 31
GnomAD3 exomes AF: 0.247 AC: 56221AN: 227246Hom.: 7863 AF XY: 0.249 AC XY: 30556AN XY: 122616
GnomAD4 exome AF: 0.283 AC: 406074AN: 1433200Hom.: 61159 Cov.: 24 AF XY: 0.281 AC XY: 199911AN XY: 712534
GnomAD4 genome AF: 0.254 AC: 38590AN: 151926Hom.: 5378 Cov.: 31 AF XY: 0.253 AC XY: 18771AN XY: 74236
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at