rs1986785

Positions:

• chr13-29455585-C-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTUS2	NM_001033602.4	c.3184+15536C>A		intron_variant		ENST00000612955.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTUS2	ENST00000612955.6	c.3184+15536C>A		intron_variant		5	NM_001033602.4
MTUS2	ENST00000380808.6	c.121+15536C>A		intron_variant		1		P1
MTUS2	ENST00000542829.1	c.-149-24565C>A		intron_variant		1

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

Gnomad4 AFR AF: 0.745

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.554

Alfa AF: 0.519 Hom.: 29843

Bravo AF: 0.569

Asia WGS AF: 0.328 AC: 1143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.20

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

Publications

LitVar

Other links and lift over

dbSNP: rs1986785; hg19: chr13-30029722;