rs775739391
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_001289125.3(IFNAR2):c.311del(p.Glu104GlyfsTer7) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000316 in 1,613,854 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. E104E) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001289125.3 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFNAR2 | NM_001289125.3 | c.311del | p.Glu104GlyfsTer7 | frameshift_variant | 5/9 | ENST00000342136.9 | |
IFNAR2-IL10RB | NM_001414505.1 | c.311del | p.Glu104GlyfsTer7 | frameshift_variant | 5/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFNAR2 | ENST00000342136.9 | c.311del | p.Glu104GlyfsTer7 | frameshift_variant | 5/9 | 1 | NM_001289125.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251418Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135902
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1461672Hom.: 0 Cov.: 31 AF XY: 0.0000289 AC XY: 21AN XY: 727150
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74332
ClinVar
Submissions by phenotype
Immunodeficiency 45 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 30, 2015 | - - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | May 13, 2023 | For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 218160). This premature translational stop signal has been observed in individual(s) with IFNAR2 deficiency (PMID: 26424569). This variant is present in population databases (rs775739391, gnomAD 0.009%). This sequence change creates a premature translational stop signal (p.Glu104Glyfs*7) in the IFNAR2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in IFNAR2 are known to be pathogenic (PMID: 26424569, 33193576). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at