rs3153
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001289125.3(IFNAR2):c.-83-4640G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 151,538 control chromosomes in the GnomAD database, including 6,670 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance,association (no stars).
Frequency
Genomes: 𝑓 0.28 ( 6670 hom., cov: 29)
Consequence
IFNAR2
NM_001289125.3 intron
NM_001289125.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.494
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFNAR2 | NM_001289125.3 | c.-83-4640G>A | intron_variant | ENST00000342136.9 | |||
IFNAR2-IL10RB | NM_001414505.1 | c.-37-4686G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFNAR2 | ENST00000342136.9 | c.-83-4640G>A | intron_variant | 1 | NM_001289125.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.279 AC: 42295AN: 151420Hom.: 6665 Cov.: 29
GnomAD3 genomes
?
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29
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.279 AC: 42326AN: 151538Hom.: 6670 Cov.: 29 AF XY: 0.291 AC XY: 21501AN XY: 74006
GnomAD4 genome
?
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42326
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29
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21501
AN XY:
74006
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1629
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3478
ClinVar
Significance: Uncertain significance; association
Submissions summary: Uncertain:1Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Associated with severe COVID-19 disease Uncertain:1
Uncertain significance, no assertion criteria provided | research | HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas | Jul 01, 2023 | - - |
Mortality risk in patients with severe coronavirus disease (COVID-19) Other:1
association, no assertion criteria provided | research | HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas | May 06, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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