NM_001033602.4:c.3117+9481G>A

Variant names:

• chr13-29368954-G-A
• rs2388092
• NM_001033602.4:c.3117+9481G>A

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+9481G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 151,994 control chromosomes in the GnomAD database, including 31,939 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 0.65 (31939 hom., cov: 31)
• Consequence: MTUS2 NM_001033602.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340
• Publications: 2 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTUS2	NM_001033602.4	MANE Select	c.3117+9481G>A		intron	N/A	NP_001028774.3
	MTUS2	NM_001384605.1		c.3117+9481G>A		intron	N/A	NP_001371534.1
	MTUS2	NM_001384606.1		c.3117+9481G>A		intron	N/A	NP_001371535.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTUS2	ENST00000612955.6	TSL:5 MANE Select	c.3117+9481G>A		intron	N/A	ENSP00000483729.2

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98149 AN: 151876 Hom.: 31909 Cov.: 31

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.646 AC: 98214 AN: 151994 Hom.: 31939 Cov.: 31 AF XY: 0.653 AC XY: 48486 AN XY: 74296

African (AFR) AF: 0.587 AC: 24302 AN: 41424

American (AMR) AF: 0.713 AC: 10892 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2088 AN: 3472

East Asian (EAS) AF: 0.749 AC: 3859 AN: 5152

South Asian (SAS) AF: 0.670 AC: 3226 AN: 4812

European-Finnish (FIN) AF: 0.717 AC: 7591 AN: 10582

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.650 AC: 44174 AN: 67952

Other (OTH) AF: 0.627 AC: 1326 AN: 2116

Alfa AF: 0.643 Hom.: 4096

Bravo AF: 0.646

Asia WGS AF: 0.738 AC: 2563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.2
DANN	Benign	0.38
PhyloP100		0.034
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: rs2388092; hg19: chr13-29943091;