rs2388082

Positions:

• chr13-29387195-C-G
• chr13-29387195-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001033602.4(MTUS2):​c.3117+27722C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,160 control chromosomes in the GnomAD database, including 1,374 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 0.13 (1374 hom., cov: 32)
• Consequence: MTUS2 NM_001033602.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTUS2	NM_001033602.4	c.3117+27722C>G		intron_variant		ENST00000612955.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTUS2	ENST00000612955.6	c.3117+27722C>G		intron_variant		5	NM_001033602.4

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19559 AN: 152042 Hom.: 1369 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.0771

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.0516

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.129 AC: 19581 AN: 152160 Hom.: 1374 Cov.: 32 AF XY: 0.125 AC XY: 9323 AN XY: 74398

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.0773

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.0516

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.136

Alfa AF: 0.118 Hom.: 602

Bravo AF: 0.133

Asia WGS AF: 0.120 AC: 415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.85
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2388082; hg19: chr13-29961332;