chr13-28954018-A-G

Position:

• chr13-28954018-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.-242-70439A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.903 in 152,174 control chromosomes in the GnomAD database, including 62,577 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 0.90 (62577 hom., cov: 33)
• Consequence: MTUS2 NM_001033602.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.346

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTUS2	NM_001033602.4	c.-242-70439A>G		intron_variant		ENST00000612955.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTUS2	ENST00000612955.6	c.-242-70439A>G		intron_variant		5	NM_001033602.4

Frequencies

GnomAD3 genomes AF: 0.903 AC: 137329 AN: 152056 Hom.: 62550 Cov.: 33

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.881

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.978

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.990

Gnomad FIN AF: 0.980

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.904

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

GnomAD4 genome AF: 0.903 AC: 137410 AN: 152174 Hom.: 62577 Cov.: 33 AF XY: 0.906 AC XY: 67415 AN XY: 74394

Gnomad4 AFR AF: 0.766

Gnomad4 AMR AF: 0.931

Gnomad4 ASJ AF: 0.978

Gnomad4 EAS AF: 0.933

Gnomad4 SAS AF: 0.990

Gnomad4 FIN AF: 0.980

Gnomad4 NFE AF: 0.956

Gnomad4 OTH AF: 0.905

Alfa AF: 0.932 Hom.: 8237

Bravo AF: 0.891

Asia WGS AF: 0.960 AC: 3334 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.3
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs647767; hg19: chr13-29528155;