rs3886729

Positions:

• chr13-29005791-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001033602.4(MTUS2):​c.-242-18666A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0237 in 152,334 control chromosomes in the GnomAD database, including 60 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 0.024 (60 hom., cov: 32)
• Consequence: MTUS2 NM_001033602.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.638

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=-0.89).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0237 (3605/152334) while in subpopulation EAS AF= 0.0521 (270/5182). AF 95% confidence interval is 0.047. There are 60 homozygotes in gnomad4. There are 1707 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 60 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MTUS2	NM_001033602.4	c.-242-18666A>G		intron_variant		ENST00000612955.6	NP_001028774.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MTUS2	ENST00000612955.6	c.-242-18666A>G		intron_variant		5	NM_001033602.4	ENSP00000483729

Frequencies

GnomAD3 genomes AF: 0.0235 AC: 3584 AN: 152216 Hom.: 58 Cov.: 32

Gnomad AFR AF: 0.0457

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0217

Gnomad ASJ AF: 0.00663

Gnomad EAS AF: 0.0518

Gnomad SAS AF: 0.00248

Gnomad FIN AF: 0.00198

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0144

Gnomad OTH AF: 0.0258

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

GnomAD4 genome AF: 0.0237 AC: 3605 AN: 152334 Hom.: 60 Cov.: 32 AF XY: 0.0229 AC XY: 1707 AN XY: 74480

Gnomad4 AFR AF: 0.0460

Gnomad4 AMR AF: 0.0216

Gnomad4 ASJ AF: 0.00663

Gnomad4 EAS AF: 0.0521

Gnomad4 SAS AF: 0.00249

Gnomad4 FIN AF: 0.00198

Gnomad4 NFE AF: 0.0144

Gnomad4 OTH AF: 0.0255

Alfa AF: 0.0171 Hom.: 7

Bravo AF: 0.0265

Asia WGS AF: 0.0210 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.57
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3886729; hg19: chr13-29579928;