rs6986402

chr8-17773080-T-C

Variant summary

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

The NM_001363059.2(MTUS1):c.-154-17119A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,110 control chromosomes in the GnomAD database, including 4,215 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 0.23 (4215 hom., cov: 32)
• Consequence: MTUS1 NM_001363059.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTUS1	NM_001363059.2	c.-154-17119A>G		intron_variant		ENST00000693296.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTUS1	ENST00000693296.1	c.-154-17119A>G		intron_variant			NM_001363059.2

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35254 AN: 151992 Hom.: 4206 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.232 AC: 35286 AN: 152110 Hom.: 4215 Cov.: 32 AF XY: 0.229 AC XY: 17051 AN XY: 74356

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.224

Alfa AF: 0.218 Hom.: 896

Bravo AF: 0.241

Asia WGS AF: 0.190 AC: 662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.63
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6986402; hg19: chr8-17630589;