rs8178435
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001414505.1(IFNAR2-IL10RB):c.710-2682A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00127 in 278,620 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0022 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00015 ( 0 hom. )
Consequence
IFNAR2-IL10RB
NM_001414505.1 intron
NM_001414505.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.590
Genes affected
IFNAR2 (HGNC:5433): (interferon alpha and beta receptor subunit 2) The protein encoded by this gene is a type I membrane protein that forms one of the two chains of a receptor for interferons alpha and beta. Binding and activation of the receptor stimulates Janus protein kinases, which in turn phosphorylate several proteins, including STAT1 and STAT2. The protein belongs to the type II cytokine receptor family. Mutations in this gene are associated with Immunodeficiency 45. [provided by RefSeq, Jul 2020]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IFNAR2 | NM_001289125.3 | c.*2212A>G | downstream_gene_variant | ENST00000342136.9 | NP_001276054.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IFNAR2-IL10RB | ENST00000433395.7 | c.710-2682A>G | intron_variant | 5 | ENSP00000388223.3 | |||||
IFNAR2 | ENST00000342136.9 | c.*2212A>G | downstream_gene_variant | 1 | NM_001289125.3 | ENSP00000343957.5 |
Frequencies
GnomAD3 genomes AF: 0.00219 AC: 333AN: 152012Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.000150 AC: 19AN: 126490Hom.: 0 Cov.: 0 AF XY: 0.000126 AC XY: 9AN XY: 71502
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GnomAD4 genome AF: 0.00220 AC: 334AN: 152130Hom.: 0 Cov.: 32 AF XY: 0.00211 AC XY: 157AN XY: 74390
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ClinVar
Not reported inComputational scores
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Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at