21-33324959-T-G

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.232
Variant links:
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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IFNAR1NM_000629.3 linkc.-97T>G upstream_gene_variant ENST00000270139.8 NP_000620.2 P17181-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IFNAR1ENST00000270139.8 linkc.-97T>G upstream_gene_variant 1 NM_000629.3 ENSP00000270139.3 P17181-1

Frequencies

GnomAD3 genomes
Cov.:
29
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
914762
Hom.:
0
Cov.:
12
AF XY:
0.00
AC XY:
0
AN XY:
462020
African (AFR)
AF:
0.00
AC:
0
AN:
22738
American (AMR)
AF:
0.00
AC:
0
AN:
33060
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
20274
East Asian (EAS)
AF:
0.00
AC:
0
AN:
33194
South Asian (SAS)
AF:
0.00
AC:
0
AN:
65688
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
43022
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4184
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
650786
Other (OTH)
AF:
0.00
AC:
0
AN:
41816
GnomAD4 genome
Cov.:
29
Alfa
AF:
0.00
Hom.:
92464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
9.2
DANN
Benign
0.43
PhyloP100
-0.23
PromoterAI
-0.34
Neutral

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs2850015; hg19: chr21-34697264; API