13-29282812-A-G

Variant names:

• chr13-29282812-A-G
• rs1414357
• NM_001033602.4:c.2806+947A>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.2806+947A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 151,972 control chromosomes in the GnomAD database, including 10,154 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 0.35 (10154 hom., cov: 32)
• Consequence: MTUS2 NM_001033602.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135
• 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTUS2	NM_001033602.4	c.2806+947A>G		intron_variant	Intron 6 of 15	ENST00000612955.6	NP_001028774.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTUS2	ENST00000612955.6	c.2806+947A>G		intron_variant	Intron 6 of 15	5	NM_001033602.4	ENSP00000483729.2

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53118 AN: 151854 Hom.: 10158 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.349 AC: 53114 AN: 151972 Hom.: 10154 Cov.: 32 AF XY: 0.343 AC XY: 25509 AN XY: 74290

African (AFR) AF: 0.183 AC: 7584 AN: 41476

American (AMR) AF: 0.350 AC: 5338 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1629 AN: 3462

East Asian (EAS) AF: 0.375 AC: 1939 AN: 5168

South Asian (SAS) AF: 0.237 AC: 1139 AN: 4810

European-Finnish (FIN) AF: 0.410 AC: 4325 AN: 10554

Middle Eastern (MID) AF: 0.383 AC: 111 AN: 290

European-Non Finnish (NFE) AF: 0.441 AC: 29977 AN: 67928

Other (OTH) AF: 0.384 AC: 811 AN: 2110

Alfa AF: 0.395 Hom.: 2976

Bravo AF: 0.341

Asia WGS AF: 0.275 AC: 956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.39
DANN	Benign	0.84
PhyloP100		-0.14
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1414357; hg19: chr13-29856949;