NM_144571.3:c.140_141delGCinsAT

Variant names:

• chr4-77774703-GC-AT
• NM_144571.3:c.140_141delGCinsAT
• CNOT6L p.Ser47Asn

Variant summary

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

The NM_144571.3(CNOT6L):​c.140_141delGCinsAT​(p.Ser47Asn) variant causes a missense change. 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 nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CNOT6L NM_144571.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.06
• Publications: 0 publications found

Genes affected

CNOT6L (HGNC:18042): (CCR4-NOT transcription complex subunit 6 like) Predicted to enable poly(A)-specific ribonuclease activity. Involved in positive regulation of cell population proliferation and positive regulation of cytoplasmic mRNA processing body assembly. Located in cytosol and nucleus. Part of CCR4-NOT complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144571.3. 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
	CNOT6L	NM_144571.3	MANE Select	c.140_141delGCinsAT	p.Ser47Asn	missense	N/A	NP_653172.2	Q96LI5-1
	CNOT6L	NM_001387842.1		c.323_324delGCinsAT	p.Ser108Asn	missense	N/A	NP_001374771.1
	CNOT6L	NM_001387843.1		c.323_324delGCinsAT	p.Ser108Asn	missense	N/A	NP_001374772.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNOT6L	ENST00000504123.7	TSL:2 MANE Select	c.140_141delGCinsAT	p.Ser47Asn	missense	N/A	ENSP00000424896.1	Q96LI5-1
	CNOT6L	ENST00000873612.1		c.140_141delGCinsAT	p.Ser47Asn	missense	N/A	ENSP00000543671.1
	CNOT6L	ENST00000512485.6	TSL:5	c.125_126delGCinsAT	p.Ser42Asn	missense	N/A	ENSP00000425571.2	H0Y9Z5

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		4.1

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: chr4-78695857;