chr13-28843347-G-A

Variant names:

• chr13-28843347-G-A
• rs1161453
• NM_001033602.4:c.-243+3497G>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+3497G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 151,978 control chromosomes in the GnomAD database, including 37,924 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 0.69 (37924 hom., cov: 31)
• Consequence: MTUS2 NM_001033602.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• 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 (NFE) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTUS2	NM_001033602.4	c.-243+3497G>A		intron_variant	Intron 2 of 15	ENST00000612955.6	NP_001028774.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTUS2	ENST00000612955.6	c.-243+3497G>A		intron_variant	Intron 2 of 15	5	NM_001033602.4	ENSP00000483729.2

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105052 AN: 151860 Hom.: 37911 Cov.: 31

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.855

Gnomad MID AF: 0.748

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.692 AC: 105109 AN: 151978 Hom.: 37924 Cov.: 31 AF XY: 0.694 AC XY: 51571 AN XY: 74290

African (AFR) AF: 0.493 AC: 20375 AN: 41370

American (AMR) AF: 0.769 AC: 11739 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.792 AC: 2747 AN: 3468

East Asian (EAS) AF: 0.523 AC: 2696 AN: 5158

South Asian (SAS) AF: 0.559 AC: 2689 AN: 4812

European-Finnish (FIN) AF: 0.855 AC: 9058 AN: 10592

Middle Eastern (MID) AF: 0.760 AC: 222 AN: 292

European-Non Finnish (NFE) AF: 0.787 AC: 53492 AN: 67994

Other (OTH) AF: 0.701 AC: 1479 AN: 2110

Alfa AF: 0.755 Hom.: 169079

Bravo AF: 0.681

Asia WGS AF: 0.530 AC: 1844 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	0.70
DANN	Benign	0.56
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs1161453; hg19: chr13-29417484;