NM_001033602.4:c.-242-79694C>G

Variant names:

• chr13-28944763-C-G
• rs327127
• NM_001033602.4:c.-242-79694C>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.-242-79694C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.864 in 152,122 control chromosomes in the GnomAD database, including 57,511 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 0.86 (57511 hom., cov: 32)
• Consequence: MTUS2 NM_001033602.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 3 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTUS2	NM_001033602.4	c.-242-79694C>G		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.-242-79694C>G		intron_variant	Intron 2 of 15	5	NM_001033602.4	ENSP00000483729.2

Frequencies

GnomAD3 genomes AF: 0.864 AC: 131328 AN: 152004 Hom.: 57489 Cov.: 32

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.995

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.956

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.857

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.864 AC: 131399 AN: 152122 Hom.: 57511 Cov.: 32 AF XY: 0.856 AC XY: 63688 AN XY: 74368

African (AFR) AF: 0.727 AC: 30131 AN: 41442

American (AMR) AF: 0.870 AC: 13305 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.956 AC: 3317 AN: 3470

East Asian (EAS) AF: 0.826 AC: 4271 AN: 5172

South Asian (SAS) AF: 0.800 AC: 3854 AN: 4820

European-Finnish (FIN) AF: 0.857 AC: 9090 AN: 10602

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.947 AC: 64394 AN: 68006

Other (OTH) AF: 0.888 AC: 1877 AN: 2114

Alfa AF: 0.891 Hom.: 7654

Bravo AF: 0.863

Asia WGS AF: 0.790 AC: 2749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.2
DANN	Benign	0.29
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs327127; hg19: chr13-29518900;