13-28860717-G-A

Variant names:

• chr13-28860717-G-A
• rs1161457
• NM_001033602.4:c.-243+20867G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001033602.4(MTUS2):​c.-243+20867G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.763 in 152,114 control chromosomes in the GnomAD database, including 45,011 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 0.76 (45011 hom., cov: 32)
• Consequence: MTUS2 NM_001033602.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001033602.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTUS2	NM_001033602.4	MANE Select	c.-243+20867G>A		intron	N/A	NP_001028774.3
	MTUS2	NM_001384605.1		c.-243+20867G>A		intron	N/A	NP_001371534.1
	MTUS2	NM_001384606.1		c.-243+40106G>A		intron	N/A	NP_001371535.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTUS2	ENST00000612955.6	TSL:5 MANE Select	c.-243+20867G>A		intron	N/A	ENSP00000483729.2

Frequencies

GnomAD3 genomes AF: 0.763 AC: 115968 AN: 151996 Hom.: 44980 Cov.: 32

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.814

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.763 AC: 116048 AN: 152114 Hom.: 45011 Cov.: 32 AF XY: 0.763 AC XY: 56760 AN XY: 74376

African (AFR) AF: 0.663 AC: 27495 AN: 41462

American (AMR) AF: 0.814 AC: 12443 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.826 AC: 2867 AN: 3472

East Asian (EAS) AF: 0.526 AC: 2715 AN: 5164

South Asian (SAS) AF: 0.563 AC: 2710 AN: 4810

European-Finnish (FIN) AF: 0.882 AC: 9354 AN: 10608

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.824 AC: 56000 AN: 68002

Other (OTH) AF: 0.760 AC: 1602 AN: 2108

Alfa AF: 0.804 Hom.: 39273

Bravo AF: 0.758

Asia WGS AF: 0.545 AC: 1898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.51
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs1161457; hg19: chr13-29434854;