13-29359446-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_Strong BP6_Moderate BP7 BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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]

ACMG classification

Verdict is Benign. Variant got -15 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_single_submitter, 1 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	UniProt
MTUS2	NM_001033602.4	c.3090C>T	p.Ala1030=	synonymous_variant	8/16	ENST00000612955.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTUS2	ENST00000612955.6	c.3090C>T	p.Ala1030=	synonymous_variant	8/16	5	NM_001033602.4

Frequencies

GnomAD3 genomes AF: 0.0213 AC: 3247 AN: 152202 Hom.: 104 Cov.: 33

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

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

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

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:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Apr 11, 2018

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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

Other links and lift over

dbSNP: rs112264341; hg19: chr13-29933583;