13-29369075-A-G

Position:

• chr13-29369075-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001033602.4(MTUS2):​c.3117+9602A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.661 in 151,558 control chromosomes in the GnomAD database, including 33,200 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 (33200 hom., cov: 31)
• Consequence: MTUS2 NM_001033602.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.232

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTUS2	NM_001033602.4	c.3117+9602A>G		intron_variant		ENST00000612955.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTUS2	ENST00000612955.6	c.3117+9602A>G		intron_variant		5	NM_001033602.4

Frequencies

GnomAD3 genomes AF: 0.661 AC: 100038 AN: 151438 Hom.: 33151 Cov.: 31

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.661 AC: 100139 AN: 151558 Hom.: 33200 Cov.: 31 AF XY: 0.666 AC XY: 49375 AN XY: 74084

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.749

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.715

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.643

Alfa AF: 0.654 Hom.: 4058

Bravo AF: 0.663

Asia WGS AF: 0.745 AC: 2587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2388093; hg19: chr13-29943212;