rs1986785

Variant names:

• chr13-29455585-C-A
• rs1986785
• NM_001033602.4:c.3184+15536C>A

Your query was ambiguous. Multiple possible variants found:

• chr13-29455585-C-A
• chr13-29455585-C-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.3184+15536C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 152,064 control chromosomes in the GnomAD database, including 24,820 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 0.55 (24820 hom., cov: 33)
• Consequence: MTUS2 NM_001033602.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001033602.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTUS2	NM_001033602.4	MANE Select	c.3184+15536C>A		intron	N/A	NP_001028774.3	Q5JR59-2
	MTUS2	NM_001384605.1		c.3184+15536C>A		intron	N/A	NP_001371534.1	Q5JR59-2
	MTUS2	NM_001384606.1		c.3184+15536C>A		intron	N/A	NP_001371535.1	Q5JR59-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTUS2	ENST00000612955.6	TSL:5 MANE Select	c.3184+15536C>A		intron	N/A	ENSP00000483729.2	Q5JR59-2
	MTUS2	ENST00000380808.6	TSL:1	c.121+15536C>A		intron	N/A	ENSP00000370186.2	Q5JR59-3
	MTUS2	ENST00000542829.1	TSL:1	c.-149-24565C>A		intron	N/A	ENSP00000445403.1	Q5JR59-4

Frequencies

GnomAD3 genomes AF: 0.553 AC: 84015 AN: 151946 Hom.: 24785 Cov.: 33

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.553 AC: 84099 AN: 152064 Hom.: 24820 Cov.: 33 AF XY: 0.544 AC XY: 40442 AN XY: 74340

African (AFR) AF: 0.745 AC: 30911 AN: 41480

American (AMR) AF: 0.525 AC: 8023 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2092 AN: 3470

East Asian (EAS) AF: 0.142 AC: 734 AN: 5176

South Asian (SAS) AF: 0.442 AC: 2129 AN: 4820

European-Finnish (FIN) AF: 0.385 AC: 4072 AN: 10564

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34264 AN: 67956

Other (OTH) AF: 0.554 AC: 1167 AN: 2108

Alfa AF: 0.523 Hom.: 70415

Bravo AF: 0.569

Asia WGS AF: 0.328 AC: 1143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.20
PhyloP100		0.11
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1986785; hg19: chr13-30029722;