rs12290989
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001572.5(IRF7):c.184-3C>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 1,542,680 control chromosomes in the GnomAD database, including 62,014 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001572.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IRF7 | NM_001572.5 | c.184-3C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000525445.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRF7 | ENST00000525445.6 | c.184-3C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001572.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.324 AC: 49210AN: 151888Hom.: 9279 Cov.: 35
GnomAD3 exomes AF: 0.250 AC: 40766AN: 163132Hom.: 6038 AF XY: 0.241 AC XY: 21576AN XY: 89642
GnomAD4 exome AF: 0.266 AC: 369805AN: 1390674Hom.: 52719 Cov.: 37 AF XY: 0.261 AC XY: 179184AN XY: 685366
GnomAD4 genome ? AF: 0.324 AC: 49262AN: 152006Hom.: 9295 Cov.: 35 AF XY: 0.313 AC XY: 23292AN XY: 74338
ClinVar
Submissions by phenotype
Immunodeficiency 39 Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 11, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 59% of patients studied by a panel of primary immunodeficiencies. Number of patients: 56. Only high quality variants are reported. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 07, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at