rs2937889

chr8-17716343-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001363059.2(MTUS1):c.2450-442C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 154,974 control chromosomes in the GnomAD database, including 3,576 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 0.21 (3537 hom., cov: 32)
  • Exomes 𝑓: 0.16 (39 hom.)
• Consequence: MTUS1 NM_001363059.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289

Genes affected

MTUS1 (HGNC:29789): (microtubule associated scaffold protein 1) This gene encodes a protein which contains a C-terminal domain able to interact with the angiotension II (AT2) receptor and a large coiled-coil region allowing dimerization. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. One of the transcript variants has been shown to encode a mitochondrial protein that acts as a tumor suppressor and partcipates in AT2 signaling pathways. Other variants may encode nuclear or transmembrane proteins but it has not been determined whether they also participate in AT2 signaling pathways. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTUS1	NM_001363059.2	c.2450-442C>T		intron_variant		ENST00000693296.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTUS1	ENST00000693296.1	c.2450-442C>T		intron_variant			NM_001363059.2

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31661 AN: 151968 Hom.: 3537 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.199

GnomAD4 exome AF: 0.162 AC: 468 AN: 2888 Hom.: 39 AF XY: 0.155 AC XY: 225 AN XY: 1452

Gnomad4 AFR exome AF: 0.100

Gnomad4 AMR exome AF: 0.184

Gnomad4 ASJ exome AF: 0.150

Gnomad4 EAS exome AF: 0.348

Gnomad4 SAS exome AF: 0.122

Gnomad4 FIN exome AF: 0.138

Gnomad4 NFE exome AF: 0.158

Gnomad4 OTH exome AF: 0.219

GnomAD4 genome AF: 0.208 AC: 31679 AN: 152086 Hom.: 3537 Cov.: 32 AF XY: 0.205 AC XY: 15209 AN XY: 74356

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.199

Alfa AF: 0.201 Hom.: 656

Bravo AF: 0.210

Asia WGS AF: 0.171 AC: 594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	2.6
Dann	Benign	0.41

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: rs2937889; hg19: chr8-17573852;