rs2904748

Variant names:

• chr8-17743403-T-C
• rs2904748
• NM_001363059.2:c.2287+201A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001363059.2(MTUS1):​c.2287+201A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 151,924 control chromosomes in the GnomAD database, including 16,921 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 0.46 (16921 hom., cov: 31)
• Consequence: MTUS1 NM_001363059.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.876
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTUS1	NM_001363059.2	c.2287+201A>G		intron_variant	Intron 3 of 14	ENST00000693296.1	NP_001349988.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTUS1	ENST00000693296.1	c.2287+201A>G		intron_variant	Intron 3 of 14		NM_001363059.2	ENSP00000509719.1

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70475 AN: 151806 Hom.: 16919 Cov.: 31

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.464 AC: 70502 AN: 151924 Hom.: 16921 Cov.: 31 AF XY: 0.458 AC XY: 34030 AN XY: 74266

African (AFR) AF: 0.364 AC: 15062 AN: 41428

American (AMR) AF: 0.528 AC: 8052 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2057 AN: 3468

East Asian (EAS) AF: 0.267 AC: 1379 AN: 5162

South Asian (SAS) AF: 0.363 AC: 1745 AN: 4808

European-Finnish (FIN) AF: 0.469 AC: 4949 AN: 10546

Middle Eastern (MID) AF: 0.599 AC: 175 AN: 292

European-Non Finnish (NFE) AF: 0.526 AC: 35710 AN: 67946

Other (OTH) AF: 0.502 AC: 1061 AN: 2114

Alfa AF: 0.514 Hom.: 40002

Bravo AF: 0.465

Asia WGS AF: 0.358 AC: 1248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.028
DANN	Benign	0.53
PhyloP100		-0.88
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2904748; hg19: chr8-17600912;