chr9-21481250-G-A
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_176891.5(IFNE):c.445C>T(p.Arg149*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,614,038 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000018 ( 0 hom. )
Consequence
IFNE
NM_176891.5 stop_gained
NM_176891.5 stop_gained
Scores
2
1
4
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.103
Genes affected
IFNE (HGNC:18163): (interferon epsilon) Predicted to enable cytokine activity and type I interferon receptor binding activity. Predicted to be involved in several processes, including B cell activation; defense response to other organism; and lymphocyte activation involved in immune response. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]
MIR31HG (HGNC:37187): (MIR31 host gene) This gene produces a long non-coding RNA that acts as a host gene for miR-31. This transcript may be involved in cellular pluripotency and regulate the differentiation of myoblasts and other tissues. This RNA was found to interact with Polycomb repressive proteins to repression transcription of genes involves in cell senescence. [provided by RefSeq, Dec 2017]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| IFNE | NM_176891.5 | c.445C>T | p.Arg149* | stop_gained | Exon 1 of 1 | ENST00000448696.4 | NP_795372.1 |
Ensembl
Frequencies
GnomAD3 genomes 0.0000131 AC: 2AN: 152112Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251246Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135758
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GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461808Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 727208
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GnomAD4 genome 0.0000131 AC: 2AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74420
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ClinVar
Not reported inComputational scores
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D
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at