13-29359446-C-T

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

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.73
Variant links:
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]

Genome browser will be placed here

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
MTUS2NM_001033602.4 linkuse as main transcriptc.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
MTUS2ENST00000612955.6 linkuse as main transcriptc.3090C>T p.Ala1030= synonymous_variant 8/165 NM_001033602.4 ENSP00000483729 Q5JR59-2

Frequencies

GnomAD3 genomes
AF:
0.0213
AC:
3247
AN:
152202
Hom.:
104
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0737
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00903
Gnomad ASJ
AF:
0.000288
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00103
Gnomad FIN
AF:
0.0000943
Gnomad MID
AF:
0.0190
Gnomad NFE
AF:
0.000176
Gnomad OTH
AF:
0.0138
GnomAD3 exomes
AF:
0.00563
AC:
1381
AN:
245078
Hom.:
35
AF XY:
0.00412
AC XY:
549
AN XY:
133224
show subpopulations
Gnomad AFR exome
AF:
0.0781
Gnomad AMR exome
AF:
0.00441
Gnomad ASJ exome
AF:
0.000704
Gnomad EAS exome
AF:
0.0000561
Gnomad SAS exome
AF:
0.000365
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000261
Gnomad OTH exome
AF:
0.00252
GnomAD4 exome
AF:
0.00235
AC:
3428
AN:
1459650
Hom.:
96
Cov.:
31
AF XY:
0.00207
AC XY:
1501
AN XY:
725932
show subpopulations
Gnomad4 AFR exome
AF:
0.0795
Gnomad4 AMR exome
AF:
0.00467
Gnomad4 ASJ exome
AF:
0.000460
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000373
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000188
Gnomad4 OTH exome
AF:
0.00470
GnomAD4 genome
AF:
0.0214
AC:
3257
AN:
152320
Hom.:
105
Cov.:
33
AF XY:
0.0212
AC XY:
1581
AN XY:
74486
show subpopulations
Gnomad4 AFR
AF:
0.0737
Gnomad4 AMR
AF:
0.00902
Gnomad4 ASJ
AF:
0.000288
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00104
Gnomad4 FIN
AF:
0.0000943
Gnomad4 NFE
AF:
0.000176
Gnomad4 OTH
AF:
0.0137
Alfa
AF:
0.00963
Hom.:
27
Bravo
AF:
0.0243
Asia WGS
AF:
0.00404
AC:
14
AN:
3478

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 submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpApr 11, 2018- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.67
CADD
Benign
0.15
DANN
Benign
0.51

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs112264341; hg19: chr13-29933583; API