rs2388092

Positions:

• chr13-29368954-G-A
• chr13-29368954-G-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+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

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MTUS2	NM_001033602.4	c.3117+9481G>A		intron_variant		ENST00000612955.6	NP_001028774.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MTUS2	ENST00000612955.6	c.3117+9481G>A		intron_variant		5	NM_001033602.4	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

Gnomad4 AFR AF: 0.587

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.749

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.717

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.627

Alfa AF: 0.646 Hom.: 3963

Bravo AF: 0.646

Asia WGS AF: 0.738 AC: 2563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.2
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2388092; hg19: chr13-29943091;