13-29369100-C-T

Variant names:

• chr13-29369100-C-T
• rs2388094
• NM_001033602.4:c.3117+9627C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001033602.4(MTUS2):​c.3117+9627C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 149,444 control chromosomes in the GnomAD database, including 32,677 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 0.66 (32677 hom., cov: 31)
• Consequence: MTUS2 NM_001033602.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.683
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001033602.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTUS2	NM_001033602.4	MANE Select	c.3117+9627C>T		intron	N/A	NP_001028774.3	Q5JR59-2
	MTUS2	NM_001384605.1		c.3117+9627C>T		intron	N/A	NP_001371534.1	Q5JR59-2
	MTUS2	NM_001384606.1		c.3117+9627C>T		intron	N/A	NP_001371535.1	Q5JR59-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTUS2	ENST00000612955.6	TSL:5 MANE Select	c.3117+9627C>T		intron	N/A	ENSP00000483729.2	Q5JR59-2
	MTUS2	ENST00000948542.1		c.3117+9627C>T		intron	N/A	ENSP00000618601.1

Frequencies

GnomAD3 genomes AF: 0.664 AC: 99208 AN: 149328 Hom.: 32629 Cov.: 31

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.562

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.652

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.665 AC: 99308 AN: 149444 Hom.: 32677 Cov.: 31 AF XY: 0.671 AC XY: 48964 AN XY: 72964

African (AFR) AF: 0.626 AC: 25578 AN: 40856

American (AMR) AF: 0.727 AC: 10931 AN: 15036

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2086 AN: 3424

East Asian (EAS) AF: 0.757 AC: 3845 AN: 5078

South Asian (SAS) AF: 0.684 AC: 3231 AN: 4726

European-Finnish (FIN) AF: 0.727 AC: 7477 AN: 10278

Middle Eastern (MID) AF: 0.556 AC: 158 AN: 284

European-Non Finnish (NFE) AF: 0.659 AC: 44062 AN: 66824

Other (OTH) AF: 0.656 AC: 1355 AN: 2066

Alfa AF: 0.647 Hom.: 50735

Bravo AF: 0.658

Asia WGS AF: 0.743 AC: 2582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.0
DANN	Benign	0.85
PhyloP100		0.68
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2388094; hg19: chr13-29943237;