11-101958337-CTC-TTA

Variant names:

• chr11-101958337-CTC-TTA
• NM_020802.4:c.676_678delCTCinsTTA
• CEP126 p.227

Variant summary

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

The NM_020802.4(CEP126):​c.676_678delCTCinsTTA​(p.227) variant causes a synonymous 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. Synonymous variant affecting the same amino acid position (i.e. L226L) has been classified as Benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CEP126 NM_020802.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.09
• Publications: 0 publications found

Genes affected

CEP126 (HGNC:29264): (centrosomal protein 126) Involved in cilium assembly; cytoplasmic microtubule organization; and mitotic spindle organization. Located in centrosome; ciliary base; and midbody. [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_020802.4. 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
	CEP126	NM_020802.4	MANE Select	c.676_678delCTCinsTTA	p.227	synonymous	N/A	NP_065853.3	Q9P2H0
	CEP126	NM_001363543.2		c.79_81delCTCinsTTA	p.28	synonymous	N/A	NP_001350472.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP126	ENST00000263468.13	TSL:1 MANE Select	c.676_678delCTCinsTTA	p.227	synonymous	N/A	ENSP00000263468.8	Q9P2H0
	CEP126	ENST00000931861.1		c.676_678delCTCinsTTA	p.227	synonymous	N/A	ENSP00000601920.1
	CEP126	ENST00000532529.1	TSL:5	n.*172_*174delCTCinsTTA		non_coding_transcript_exon	Exon 4 of 10	ENSP00000433643.1	H0YDI0

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		5.1

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: chr11-101829068;