NM_001141947.3:c.-21_-20insGTAAGCAGGG

Variant names:

• chr3-56557220-T-TGGGTAAGCAG
• NM_001141947.3:c.-21_-20insGTAAGCAGGG

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001141947.3(CCDC66):​c.-21_-20insGTAAGCAGGG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CCDC66 NM_001141947.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376
• Publications: 0 publications found

Genes affected

CCDC66 (HGNC:27709): (coiled-coil domain containing 66) Enables microtubule binding activity. Involved in cilium assembly; microtubule bundle formation; and regulation of protein localization to cilium. Located in several cellular components, including Flemming body; microtubule cytoskeleton; and photoreceptor inner segment. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001141947.3. 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
	CCDC66	NM_001141947.3	MANE Select	c.-21_-20insGTAAGCAGGG		5_prime_UTR	Exon 1 of 18	NP_001135419.1
	CCDC66	NM_001353147.1		c.-21_-20insGTAAGCAGGG		5_prime_UTR	Exon 1 of 18	NP_001340076.1
	CCDC66	NM_001353148.1		c.-21_-20insGTAAGCAGGG		5_prime_UTR	Exon 1 of 18	NP_001340077.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC66	ENST00000394672.8	TSL:1 MANE Select	c.-21_-20insGTAAGCAGGG		5_prime_UTR	Exon 1 of 18	ENSP00000378167.3
	CCDC66	ENST00000326595.11	TSL:1	c.-104_-103insGTAAGCAGGG		5_prime_UTR	Exon 1 of 18	ENSP00000326050.7
	CCDC66	ENST00000341455.10	TSL:1	n.-21_-20insGTAAGCAGGG		non_coding_transcript_exon	Exon 1 of 18	ENSP00000343840.6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.38

Splicing

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

Other links and lift over

hg19: chr3-56591248;