21-33324959-T-G
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001384504.1(IFNAR1):c.-132+321T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 29)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
IFNAR1
NM_001384504.1 intron
NM_001384504.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.232
Genes affected
IFNAR1 (HGNC:5432): (interferon alpha and beta receptor subunit 1) 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 and functions as an antiviral factor. [provided by RefSeq, Jul 2020]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 29
GnomAD3 genomes
Cov.:
29
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 914762Hom.: 0 Cov.: 12 AF XY: 0.00 AC XY: 0AN XY: 462020
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
914762
Hom.:
Cov.:
12
AF XY:
AC XY:
0
AN XY:
462020
African (AFR)
AF:
AC:
0
AN:
22738
American (AMR)
AF:
AC:
0
AN:
33060
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
20274
East Asian (EAS)
AF:
AC:
0
AN:
33194
South Asian (SAS)
AF:
AC:
0
AN:
65688
European-Finnish (FIN)
AF:
AC:
0
AN:
43022
Middle Eastern (MID)
AF:
AC:
0
AN:
4184
European-Non Finnish (NFE)
AF:
AC:
0
AN:
650786
Other (OTH)
AF:
AC:
0
AN:
41816
GnomAD4 genome Cov.: 29
GnomAD4 genome
Cov.:
29
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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