rs11840712

chr13-29315305-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.2807-9308A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,154 control chromosomes in the GnomAD database, including 2,614 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 0.17 (2614 hom., cov: 32)
• Consequence: MTUS2 NM_001033602.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.484

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=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTUS2	NM_001033602.4	c.2807-9308A>G		intron_variant		ENST00000612955.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTUS2	ENST00000612955.6	c.2807-9308A>G		intron_variant		5	NM_001033602.4

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25961 AN: 152034 Hom.: 2602 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.171 AC: 26005 AN: 152154 Hom.: 2614 Cov.: 32 AF XY: 0.177 AC XY: 13176 AN XY: 74404

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.197

Alfa AF: 0.153 Hom.: 263

Bravo AF: 0.180

Asia WGS AF: 0.306 AC: 1064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	12
Dann	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11840712; hg19: chr13-29889442;