13-29359446-C-T
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001033602.4(MTUS2):c.3090C>T(p.Ala1030=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00415 in 1,611,970 control chromosomes in the GnomAD database, including 201 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.021 ( 105 hom., cov: 33)
Exomes 𝑓: 0.0023 ( 96 hom. )
Consequence
MTUS2
NM_001033602.4 synonymous
NM_001033602.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.73
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 Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
Variant 13-29359446-C-T is Benign according to our data. Variant chr13-29359446-C-T is described in ClinVar as [Benign]. Clinvar id is 781098.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-1.73 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0715 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTUS2 | NM_001033602.4 | c.3090C>T | p.Ala1030= | synonymous_variant | 8/16 | ENST00000612955.6 | NP_001028774.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MTUS2 | ENST00000612955.6 | c.3090C>T | p.Ala1030= | synonymous_variant | 8/16 | 5 | NM_001033602.4 | ENSP00000483729 |
Frequencies
GnomAD3 genomes AF: 0.0213 AC: 3247AN: 152202Hom.: 104 Cov.: 33
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GnomAD3 exomes AF: 0.00563 AC: 1381AN: 245078Hom.: 35 AF XY: 0.00412 AC XY: 549AN XY: 133224
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GnomAD4 exome AF: 0.00235 AC: 3428AN: 1459650Hom.: 96 Cov.: 31 AF XY: 0.00207 AC XY: 1501AN XY: 725932
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GnomAD4 genome AF: 0.0214 AC: 3257AN: 152320Hom.: 105 Cov.: 33 AF XY: 0.0212 AC XY: 1581AN XY: 74486
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 11, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at