rs461093
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002462.5(MX1):c.-98+397C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 152,216 control chromosomes in the GnomAD database, including 7,949 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 0.31 ( 7948 hom., cov: 33)
Exomes 𝑓: 0.39 ( 1 hom. )
Consequence
MX1
NM_002462.5 intron
NM_002462.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.212
Genes affected
MX1 (HGNC:7532): (MX dynamin like GTPase 1) This gene encodes a guanosine triphosphate (GTP)-metabolizing protein that participates in the cellular antiviral response. The encoded protein is induced by type I and type II interferons and antagonizes the replication process of several different RNA and DNA viruses. There is a related gene located adjacent to this gene on chromosome 21, and there are multiple pseudogenes located in a cluster on chromosome 4. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]
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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=-0.87).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MX1 | NM_002462.5 | c.-98+397C>G | intron_variant | ENST00000398598.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MX1 | ENST00000398598.8 | c.-98+397C>G | intron_variant | 1 | NM_002462.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.315 AC: 47933AN: 152080Hom.: 7952 Cov.: 33
GnomAD3 genomes
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GnomAD4 exome AF: 0.389 AC: 7AN: 18Hom.: 1 Cov.: 0 AF XY: 0.333 AC XY: 4AN XY: 12
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GnomAD4 genome ? AF: 0.315 AC: 47926AN: 152198Hom.: 7948 Cov.: 33 AF XY: 0.318 AC XY: 23694AN XY: 74396
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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