13-29244656-A-G

Variant names:

• chr13-29244656-A-G
• rs9314945
• NM_001033602.4:c.2645-37048A>G

Variant summary

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

The NM_001033602.4(MTUS2):​c.2645-37048A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.932 in 152,172 control chromosomes in the GnomAD database, including 66,938 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 0.93 (66938 hom., cov: 31)
• Consequence: MTUS2 NM_001033602.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457
• Publications: 0 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]

MTUS2-AS2 (HGNC:40923): (MTUS2 antisense RNA 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.992 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.2645-37048A>G		intron	N/A	NP_001028774.3
	MTUS2	NM_001384605.1		c.2645-37048A>G		intron	N/A	NP_001371534.1
	MTUS2	NM_001384606.1		c.2645-37048A>G		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.2645-37048A>G		intron	N/A	ENSP00000483729.2
	MTUS2	ENST00000255289.5	TSL:4	n.387-37048A>G		intron	N/A
	MTUS2-AS2	ENST00000417624.5	TSL:3	n.141-1958T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.932 AC: 141782 AN: 152054 Hom.: 66919 Cov.: 31

Gnomad AFR AF: 0.767

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.974

Gnomad ASJ AF: 0.990

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.999

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.948

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

GnomAD4 genome AF: 0.932 AC: 141852 AN: 152172 Hom.: 66938 Cov.: 31 AF XY: 0.934 AC XY: 69527 AN XY: 74438

African (AFR) AF: 0.766 AC: 31766 AN: 41446

American (AMR) AF: 0.974 AC: 14903 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.990 AC: 3436 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5167 AN: 5168

South Asian (SAS) AF: 0.999 AC: 4812 AN: 4818

European-Finnish (FIN) AF: 1.00 AC: 10618 AN: 10618

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.999 AC: 67946 AN: 68030

Other (OTH) AF: 0.949 AC: 2006 AN: 2114

Alfa AF: 0.983 Hom.: 9561

Bravo AF: 0.922

Asia WGS AF: 0.984 AC: 3421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.5
DANN	Benign	0.12
PhyloP100		-0.46
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: rs9314945; hg19: chr13-29818793;