rs1059479

Variant names:

• chr1-112701270-T-G
• rs1059479
• NM_175744.5:c.*270A>C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_175744.5(RHOC):​c.*270A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: RHOC NM_175744.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.245
• Publications: 4 publications found

Genes affected

RHOC (HGNC:669): (ras homolog family member C) This gene encodes a member of the Rho family of small GTPases, which cycle between inactive GDP-bound and active GTP-bound states and function as molecular switches in signal transduction cascades. Rho proteins promote reorganization of the actin cytoskeleton and regulate cell shape, attachment, and motility. The protein encoded by this gene is prenylated at its C-terminus, and localizes to the cytoplasm and plasma membrane. It is thought to be important in cell locomotion. Overexpression of this gene is associated with tumor cell proliferation and metastasis. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jul 2008]

MOV10 (HGNC:7200): (Mov10 RNA helicase) Enables 5'-3' RNA helicase activity and RNA binding activity. Involved in defense response to virus; negative regulation of transposition, RNA-mediated; and posttranscriptional regulation of gene expression. Located in P-body and cytosol. Implicated in hypertension. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_175744.5. 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
	RHOC	NM_175744.5	MANE Select	c.*270A>C		3_prime_UTR	Exon 6 of 6	NP_786886.1	P08134
	RHOC	NM_001042678.2		c.*270A>C		3_prime_UTR	Exon 5 of 5	NP_001036143.1	P08134
	RHOC	NM_001042679.2		c.*270A>C		3_prime_UTR	Exon 6 of 6	NP_001036144.1	P08134

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RHOC	ENST00000339083.12	TSL:1 MANE Select	c.*270A>C		3_prime_UTR	Exon 6 of 6	ENSP00000345236.8	P08134
	RHOC	ENST00000369642.7	TSL:1	c.*270A>C		3_prime_UTR	Exon 5 of 5	ENSP00000358656.3	P08134
	MOV10	ENST00000885023.1		c.*763T>G		3_prime_UTR	Exon 21 of 21	ENSP00000555082.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 9

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	20
DANN	Benign	0.79
PhyloP100		0.24

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: rs1059479; hg19: chr1-113243892;