10-23008322-CG-TT

Variant names:

• chr10-23008322-CG-TT
• NM_173081.5:c.1876_1877delCGinsTT
• ARMC3 p.Arg626Leu

Variant summary

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

The NM_173081.5(ARMC3):​c.1876_1877delCGinsTT​(p.Arg626Leu) 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.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ARMC3 NM_173081.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.02
• Publications: 0 publications found

Genes affected

ARMC3 (HGNC:30964): (armadillo repeat containing 3) Armadillo/beta-catenin (CTNNB1; MIM 116806)-like (ARM) domains are imperfect 45-amino acid repeats involved in protein-protein interactions. ARM domain-containing proteins, such as ARMC3, function in signal transduction, development, cell adhesion and mobility, and tumor initiation and metastasis (Li et al., 2006 [PubMed 16915934]).[supplied by OMIM, Mar 2008]

ENSG00000286924 (HGNC:):

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173081.5. 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
	ARMC3	NM_173081.5	MANE Select	c.1876_1877delCGinsTT	p.Arg626Leu	missense	N/A	NP_775104.2	Q5W041-2
	ARMC3	NM_001282745.2		c.1876_1877delCGinsTT	p.Arg626Leu	missense	N/A	NP_001269674.1	Q5W041-4
	ARMC3	NM_001282746.2		c.1876_1877delCGinsTT	p.Arg626Leu	missense	N/A	NP_001269675.1	Q5W041-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARMC3	ENST00000298032.10	TSL:1 MANE Select	c.1876_1877delCGinsTT	p.Arg626Leu	missense	N/A	ENSP00000298032.5	Q5W041-2
	ARMC3	ENST00000409049.7	TSL:1	c.1876_1877delCGinsTT	p.Arg626Leu	missense	N/A	ENSP00000387288.3	Q5W041-3
	ARMC3	ENST00000409983.7	TSL:2	c.1876_1877delCGinsTT	p.Arg626Leu	missense	N/A	ENSP00000386943.3	Q5W041-4

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		3.0

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: chr10-23297251;