rs2388094
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001033602.4(MTUS2):c.3117+9627C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000535 in 149,418 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000054 ( 0 hom., cov: 31)
Consequence
MTUS2
NM_001033602.4 intron
NM_001033602.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.683
Genes affected
MTUS2 (HGNC:20595): (microtubule associated scaffold protein 2) Enables microtubule binding activity and protein homodimerization activity. Part of nucleus. Colocalizes with centrosome and cytoplasmic microtubule. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTUS2 | NM_001033602.4 | c.3117+9627C>A | intron_variant | ENST00000612955.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTUS2 | ENST00000612955.6 | c.3117+9627C>A | intron_variant | 5 | NM_001033602.4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000535 AC: 8AN: 149418Hom.: 0 Cov.: 31
GnomAD3 genomes
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31
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GnomAD4 genome ? AF: 0.0000535 AC: 8AN: 149418Hom.: 0 Cov.: 31 AF XY: 0.0000823 AC XY: 6AN XY: 72880
GnomAD4 genome
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72880
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at