rs457274
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001144925.2(MX1):c.-982C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 152,148 control chromosomes in the GnomAD database, including 10,591 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 0.35 ( 10587 hom., cov: 33)
Exomes 𝑓: 0.36 ( 4 hom. )
Consequence
MX1
NM_001144925.2 5_prime_UTR
NM_001144925.2 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0510
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=-1.06).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MX1 | NM_001144925.2 | c.-982C>G | 5_prime_UTR_variant | 1/19 | |||
MX1 | XM_011529568.3 | c.-879C>G | 5_prime_UTR_variant | 1/20 | |||
MX1 | XM_017028349.3 | c.-1001C>G | 5_prime_UTR_variant | 1/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MX1 | ENST00000398600.6 | c.-982C>G | 5_prime_UTR_variant | 1/19 | 2 | P1 | |||
MX1 | ENST00000679445.1 | c.-586+118C>G | intron_variant | P1 | |||||
MX1 | ENST00000679464.1 | c.-624+118C>G | intron_variant | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.352 AC: 53551AN: 151954Hom.: 10588 Cov.: 33
GnomAD3 genomes
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GnomAD4 exome AF: 0.355 AC: 27AN: 76Hom.: 4 Cov.: 0 AF XY: 0.440 AC XY: 22AN XY: 50
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GnomAD4 genome ? AF: 0.352 AC: 53566AN: 152072Hom.: 10587 Cov.: 33 AF XY: 0.357 AC XY: 26548AN XY: 74314
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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