chr13-29369100-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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 -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTUS2	NM_001033602.4	c.3117+9627C>T		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.3117+9627C>T		intron_variant	Intron 8 of 15	5	NM_001033602.4	ENSP00000483729.2

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

Gnomad4 AFR AF: 0.626

Gnomad4 AMR AF: 0.727

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.684

Gnomad4 FIN AF: 0.727

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.656

Alfa AF: 0.644 Hom.: 39160

Bravo AF: 0.658

Asia WGS AF: 0.743 AC: 2582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.0
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2388094; hg19: chr13-29943237;