13-29046517-A-G

Position:

• chr13-29046517-A-G

Variant summary

Our verdict is Benign. Variant got -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

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=-1.07).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MTUS2	NM_001033602.4	c.2446+12392A>G		intron_variant		ENST00000612955.6	NP_001028774.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MTUS2	ENST00000612955.6	c.2446+12392A>G		intron_variant		5	NM_001033602.4	ENSP00000483729.2

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

Gnomad4 AFR AF: 0.902

Gnomad4 AMR AF: 0.973

Gnomad4 ASJ AF: 0.982

Gnomad4 EAS AF: 0.887

Gnomad4 SAS AF: 0.976

Gnomad4 FIN AF: 0.989

Gnomad4 NFE AF: 0.981

Gnomad4 OTH AF: 0.948

Alfa AF: 0.975 Hom.: 5864

Bravo AF: 0.951

Asia WGS AF: 0.921 AC: 3204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.2
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2479768; hg19: chr13-29620654;