13-29046517-A-G

Variant names:

• chr13-29046517-A-G
• rs2479768
• NM_001033602.4:c.2446+12392A>G

Variant summary

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

The NM_001033602.4(MTUS2):​c.2446+12392A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.955 in 152,292 control chromosomes in the GnomAD database, including 69,598 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 0.96 (69598 hom., cov: 33)
• Consequence: MTUS2 NM_001033602.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• 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=-1.07).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.974 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTUS2	NM_001033602.4	MANE Select	c.2446+12392A>G		intron	N/A	NP_001028774.3	Q5JR59-2
	MTUS2	NM_001384605.1		c.2446+12392A>G		intron	N/A	NP_001371534.1	Q5JR59-2
	MTUS2	NM_001384606.1		c.2446+12392A>G		intron	N/A	NP_001371535.1	Q5JR59-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTUS2	ENST00000612955.6	TSL:5 MANE Select	c.2446+12392A>G		intron	N/A	ENSP00000483729.2	Q5JR59-2
	MTUS2	ENST00000948542.1		c.2446+12392A>G		intron	N/A	ENSP00000618601.1

Frequencies

GnomAD3 genomes AF: 0.955 AC: 145396 AN: 152174 Hom.: 69565 Cov.: 33

Gnomad AFR AF: 0.902

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.973

Gnomad ASJ AF: 0.982

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.976

Gnomad FIN AF: 0.989

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.981

Gnomad OTH AF: 0.949

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

GnomAD4 genome AF: 0.955 AC: 145484 AN: 152292 Hom.: 69598 Cov.: 33 AF XY: 0.956 AC XY: 71191 AN XY: 74474

African (AFR) AF: 0.902 AC: 37465 AN: 41540

American (AMR) AF: 0.973 AC: 14895 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.982 AC: 3411 AN: 3472

East Asian (EAS) AF: 0.887 AC: 4582 AN: 5166

South Asian (SAS) AF: 0.976 AC: 4712 AN: 4826

European-Finnish (FIN) AF: 0.989 AC: 10506 AN: 10626

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.981 AC: 66714 AN: 68040

Other (OTH) AF: 0.948 AC: 2005 AN: 2114

Alfa AF: 0.950 Hom.: 33521

Bravo AF: 0.951

Asia WGS AF: 0.921 AC: 3204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.2
DANN	Benign	0.24
PhyloP100		-1.8
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: rs2479768; hg19: chr13-29620654;