3-56557199-A-AGTAAGCAGGGGTAAGCAGGG

Variant names:

• chr3-56557199-A-AGTAAGCAGGGGTAAGCAGGG
• NM_001141947.3:c.-44_-43insGTAAGCAGGGGTAAGCAGGG

Variant summary

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

The NM_001141947.3(CCDC66):​c.-44_-43insGTAAGCAGGGGTAAGCAGGG 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. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, 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: CCDC66 NM_001141947.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.51
• 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 0 ACMG points.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC66	NM_001141947.3	MANE Select	c.-44_-43insGTAAGCAGGGGTAAGCAGGG		5_prime_UTR	Exon 1 of 18	NP_001135419.1
	CCDC66	NR_024460.2		n.44_45insGTAAGCAGGGGTAAGCAGGG		non_coding_transcript_exon	Exon 1 of 18
	CCDC66	NR_148366.1		n.44_45insGTAAGCAGGGGTAAGCAGGG		non_coding_transcript_exon	Exon 1 of 19

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC66	ENST00000394672.8	TSL:1 MANE Select	c.-44_-43insGTAAGCAGGGGTAAGCAGGG		5_prime_UTR	Exon 1 of 18	ENSP00000378167.3
	CCDC66	ENST00000326595.11	TSL:1	c.-127_-126insGTAAGCAGGGGTAAGCAGGG		5_prime_UTR	Exon 1 of 18	ENSP00000326050.7
	CCDC66	ENST00000439445.5	TSL:3	n.-44_-43insGTAAGCAGGGGTAAGCAGGG		non_coding_transcript_exon	Exon 1 of 6	ENSP00000390652.1

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		2.5

Splicing

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

Other links and lift over

hg19: chr3-56591227;