13-29416829-T-G

Variant names:

• chr13-29416829-T-G
• rs3125719
• NM_001033602.4:c.3118-23154T>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.3118-23154T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 91,906 control chromosomes in the GnomAD database, including 9,257 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 0.51 (9257 hom., cov: 23)
• Consequence: MTUS2 NM_001033602.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.478
• Publications: 1 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTUS2	NM_001033602.4	c.3118-23154T>G		intron_variant	Intron 8 of 15	ENST00000612955.6	NP_001028774.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTUS2	ENST00000612955.6	c.3118-23154T>G		intron_variant	Intron 8 of 15	5	NM_001033602.4	ENSP00000483729.2

Frequencies

GnomAD3 genomes AF: 0.507 AC: 46553 AN: 91782 Hom.: 9231 Cov.: 23

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.507 AC: 46635 AN: 91906 Hom.: 9257 Cov.: 23 AF XY: 0.510 AC XY: 22873 AN XY: 44878

African (AFR) AF: 0.629 AC: 23262 AN: 36990

American (AMR) AF: 0.481 AC: 3875 AN: 8056

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 419 AN: 1338

East Asian (EAS) AF: 0.504 AC: 1111 AN: 2204

South Asian (SAS) AF: 0.414 AC: 911 AN: 2198

European-Finnish (FIN) AF: 0.492 AC: 3002 AN: 6102

Middle Eastern (MID) AF: 0.391 AC: 50 AN: 128

European-Non Finnish (NFE) AF: 0.399 AC: 13342 AN: 33404

Other (OTH) AF: 0.465 AC: 563 AN: 1210

Alfa AF: 0.611 Hom.: 7785

Asia WGS AF: 0.259 AC: 884 AN: 3410

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.78
DANN	Benign	0.45
PhyloP100		0.48
Mutation Taster		=11/89	disease causing

Splicing

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

Other links and lift over

dbSNP: rs3125719; hg19: chr13-29990966; COSMIC: COSV70916007;