3-14714110-CTA-GTT

Variant names:

• chr3-14714110-CTA-GTT
• NM_032137.5:c.1264_1266delCTAinsGTT
• C3orf20 p.Leu422Val

Variant summary

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

The NM_032137.5(C3orf20):​c.1264_1266delCTAinsGTT​(p.Leu422Val) 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: C3orf20 NM_032137.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.63
• Publications: 0 publications found

Genes affected

C3orf20 (HGNC:25320): (chromosome 3 open reading frame 20) Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

C3orf20 Gene-Disease associations (from GenCC):

• neuromyelitis optica

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032137.5. 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
	C3orf20	NM_032137.5	MANE Select	c.1264_1266delCTAinsGTT	p.Leu422Val	missense	N/A	NP_115513.4
	C3orf20	NM_001184957.2		c.898_900delCTAinsGTT	p.Leu300Val	missense	N/A	NP_001171886.1	Q8ND61-2
	C3orf20	NM_001184958.2		c.898_900delCTAinsGTT	p.Leu300Val	missense	N/A	NP_001171887.1	Q8ND61-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C3orf20	ENST00000253697.8	TSL:1 MANE Select	c.1264_1266delCTAinsGTT	p.Leu422Val	missense	N/A	ENSP00000253697.3	Q8ND61-1
	C3orf20	ENST00000412910.1	TSL:1	c.898_900delCTAinsGTT	p.Leu300Val	missense	N/A	ENSP00000396081.1	Q8ND61-2
	C3orf20	ENST00000435614.5	TSL:1	c.898_900delCTAinsGTT	p.Leu300Val	missense	N/A	ENSP00000402933.1	Q8ND61-2

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		1.6

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: chr3-14755617;