rs7842088

chr8-17727620-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.2288-3787C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.687 in 152,160 control chromosomes in the GnomAD database, including 36,612 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 0.69 (36612 hom., cov: 33)
• Consequence: MTUS1 NM_001363059.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTUS1	NM_001363059.2	c.2288-3787C>T		intron_variant		ENST00000693296.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTUS1	ENST00000693296.1	c.2288-3787C>T		intron_variant			NM_001363059.2

Frequencies

GnomAD3 genomes AF: 0.687 AC: 104411 AN: 152042 Hom.: 36561 Cov.: 33

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.687 AC: 104526 AN: 152160 Hom.: 36612 Cov.: 33 AF XY: 0.682 AC XY: 50761 AN XY: 74376

Gnomad4 AFR AF: 0.802

Gnomad4 AMR AF: 0.722

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.637

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.733

Alfa AF: 0.660 Hom.: 46128

Bravo AF: 0.701

Asia WGS AF: 0.546 AC: 1904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.47
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7842088; hg19: chr8-17585129;