rs2388093

Variant names:

• chr13-29369075-A-G
• rs2388093
• NM_001033602.4:c.3117+9602A>G

Your query was ambiguous. Multiple possible variants found:

• chr13-29369075-A-G
• chr13-29369075-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.91).
• 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 rank	MANE	Protein	UniProt
MTUS2	NM_001033602.4	c.3117+9602A>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.3117+9602A>G		intron_variant	Intron 8 of 15	5	NM_001033602.4	ENSP00000483729.2

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

African (AFR) AF: 0.638 AC: 26361 AN: 41320

American (AMR) AF: 0.719 AC: 10960 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2088 AN: 3466

East Asian (EAS) AF: 0.749 AC: 3852 AN: 5140

South Asian (SAS) AF: 0.670 AC: 3229 AN: 4816

European-Finnish (FIN) AF: 0.715 AC: 7503 AN: 10492

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.650 AC: 44048 AN: 67788

Other (OTH) AF: 0.643 AC: 1355 AN: 2106

Alfa AF: 0.653 Hom.: 4213

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
PhyloP100		-0.23
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: rs2388093; hg19: chr13-29943212;