rs2937889

Variant names:

• chr8-17716343-G-A
• rs2937889
• NM_001363059.2:c.2450-442C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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]

ENSG00000301996 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001363059.2. 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
	MTUS1	NM_001363059.2	MANE Select	c.2450-442C>T		intron	N/A	NP_001349988.1	Q9ULD2-1
	MTUS1	NM_001363057.2		c.2450-442C>T		intron	N/A	NP_001349986.1
	MTUS1	NM_001001924.3		c.2450-442C>T		intron	N/A	NP_001001924.1	Q9ULD2-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTUS1	ENST00000693296.1	MANE Select	c.2450-442C>T		intron	N/A	ENSP00000509719.1	Q9ULD2-1
	MTUS1	ENST00000262102.10	TSL:1	c.2450-442C>T		intron	N/A	ENSP00000262102.6	Q9ULD2-1
	MTUS1	ENST00000520196.5	TSL:1	n.*198-442C>T		intron	N/A	ENSP00000431016.1	H0YC63

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

African (AFR) AF: 0.100 AC: 6 AN: 60

American (AMR) AF: 0.184 AC: 25 AN: 136

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 12 AN: 80

East Asian (EAS) AF: 0.348 AC: 16 AN: 46

South Asian (SAS) AF: 0.122 AC: 12 AN: 98

European-Finnish (FIN) AF: 0.138 AC: 13 AN: 94

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4

European-Non Finnish (NFE) AF: 0.158 AC: 352 AN: 2224

Other (OTH) AF: 0.219 AC: 32 AN: 146

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

African (AFR) AF: 0.286 AC: 11857 AN: 41468

American (AMR) AF: 0.151 AC: 2306 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 630 AN: 3468

East Asian (EAS) AF: 0.266 AC: 1376 AN: 5166

South Asian (SAS) AF: 0.148 AC: 713 AN: 4826

European-Finnish (FIN) AF: 0.176 AC: 1866 AN: 10586

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12376 AN: 67958

Other (OTH) AF: 0.199 AC: 419 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.6
DANN	Benign	0.41
PhyloP100		-0.29
Mutation Taster		=99/1	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: rs2937889; hg19: chr8-17573852;