rs2039381
Variant names:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_176891.5(IFNE):c.211C>T(p.Gln71*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0218 in 1,614,016 control chromosomes in the GnomAD database, including 2,126 homozygotes. 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 0.039 ( 287 hom., cov: 32)
Exomes 𝑓: 0.020 ( 1839 hom. )
Consequence
IFNE
NM_176891.5 stop_gained
NM_176891.5 stop_gained
Scores
1
2
4
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.205
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 Benign. Variant got -8 ACMG points.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IFNE | NM_176891.5 | c.211C>T | p.Gln71* | stop_gained | Exon 1 of 1 | ENST00000448696.4 | NP_795372.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0387 AC: 5894AN: 152154Hom.: 287 Cov.: 32
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GnomAD3 exomes AF: 0.0454 AC: 11338AN: 249716Hom.: 738 AF XY: 0.0472 AC XY: 6368AN XY: 134962
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GnomAD4 exome AF: 0.0200 AC: 29258AN: 1461742Hom.: 1839 Cov.: 32 AF XY: 0.0231 AC XY: 16814AN XY: 727168
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GnomAD4 genome AF: 0.0388 AC: 5901AN: 152274Hom.: 287 Cov.: 32 AF XY: 0.0423 AC XY: 3153AN XY: 74464
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Not reported inComputational scores
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Name
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Benign
T
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Vest4
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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