rs3886729

Variant names:

• chr13-29005791-A-G
• rs3886729
• NM_001033602.4:c.-242-18666A>G

Your query was ambiguous. Multiple possible variants found:

• chr13-29005791-A-G
• chr13-29005791-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-0.89).
• 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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 60 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTUS2	NM_001033602.4	c.-242-18666A>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.-242-18666A>G		intron_variant	Intron 2 of 15	5	NM_001033602.4	ENSP00000483729.2

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

African (AFR) AF: 0.0460 AC: 1911 AN: 41566

American (AMR) AF: 0.0216 AC: 331 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.00663 AC: 23 AN: 3468

East Asian (EAS) AF: 0.0521 AC: 270 AN: 5182

South Asian (SAS) AF: 0.00249 AC: 12 AN: 4828

European-Finnish (FIN) AF: 0.00198 AC: 21 AN: 10628

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0144 AC: 980 AN: 68034

Other (OTH) AF: 0.0255 AC: 54 AN: 2114

Alfa AF: 0.0188 Hom.: 80

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
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs3886729; hg19: chr13-29579928;