16-668215-CGC-GGA

Variant names:

• chr16-668215-CGC-GGA
• NM_138769.3:c.16_18delCGCinsGGA
• RHOT2 p.Arg6Gly

Variant summary

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

The NM_138769.3(RHOT2):​c.16_18delCGCinsGGA​(p.Arg6Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R6L) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: RHOT2 NM_138769.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35
• Publications: 0 publications found

Genes affected

RHOT2 (HGNC:21169): (ras homolog family member T2) This gene encodes a member of the Rho family of GTPases. The encoded protein is localized to the outer mitochondrial membrane and plays a role in mitochondrial trafficking and fusion-fission dynamics. [provided by RefSeq, Nov 2011]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138769.3. 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
	RHOT2	NM_138769.3	MANE Select	c.16_18delCGCinsGGA	p.Arg6Gly	missense	N/A	NP_620124.1	Q8IXI1-1
	RHOT2	NM_001352275.2		c.16_18delCGCinsGGA	p.Arg6Gly	missense	N/A	NP_001339204.1	A0A8V8TM48
	RHOT2	NM_001352276.2		c.16_18delCGCinsGGA	p.Arg6Gly	missense	N/A	NP_001339205.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RHOT2	ENST00000315082.9	TSL:1 MANE Select	c.16_18delCGCinsGGA	p.Arg6Gly	missense	N/A	ENSP00000321971.4	Q8IXI1-1
	RHOT2	ENST00000697194.1		c.16_18delCGCinsGGA	p.Arg6Gly	missense	N/A	ENSP00000513180.1	A0A8V8TM48
	RHOT2	ENST00000958324.1		c.16_18delCGCinsGGA	p.Arg6Gly	missense	N/A	ENSP00000628383.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr16-718215;