dbSNP rs771732758: CCDC40:c.29+1_29+13delGTAAGCCGGGCCG (chr17-80036684-GCGGGCCGGTAAGC-G) – ACMG Classification: Likely_pathogenic (8 pts)

Variant summary

Our verdict is Likely pathogenic. The variant received 8 ACMG points: 8P and 0B. PVS1

The NM_017950.4(CCDC40):c.29+1_29+13delGTAAGCCGGGCCG variant causes a splice donor, splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000763 in 1,310,102 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_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)

Exomes 𝑓: 7.6e-7 ( 0 hom. )

Consequence

CCDC40
NM_017950.4 splice_donor, splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.31

Publications

0 publications found

Variant links:

Genes affected

CCDC40 (HGNC:26090): (coiled-coil domain 40 molecular ruler complex subunit) This gene encodes a protein that is necessary for motile cilia function. It functions in correct left-right axis formation by regulating the assembly of the inner dynein arm and the dynein regulatory complexes, which control ciliary beat. Mutations in this gene cause ciliary dyskinesia type 15, a disorder due to defects in cilia motility. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]

CCDC40 Gene-Disease associations (from GenCC):

primary ciliary dyskinesia 15
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, ClinGen, Ambry Genetics, Labcorp Genetics (formerly Invitae), PanelApp Australia, Laboratory for Molecular Medicine
primary ciliary dyskinesia
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
autoimmune disease
Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

CCDC40 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_pathogenic. The variant received 8 ACMG points.

PVS1

Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017950.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CCDC40	NM_017950.4	MANE Select	c.29+1_29+13delGTAAGCCGGGCCG	splice_donor splice_region intron	N/A	NP_060420.2
CCDC40	NM_001243342.2		c.29+1_29+13delGTAAGCCGGGCCG	splice_donor splice_region intron	N/A	NP_001230271.1
CCDC40	NM_001330508.2		c.29+1_29+13delGTAAGCCGGGCCG	splice_donor splice_region intron	N/A	NP_001317437.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CCDC40	ENST00000397545.9	TSL:5 MANE Select	c.29+1_29+13delGTAAGCCGGGCCG	splice_donor splice_region intron	N/A	ENSP00000380679.4
CCDC40	ENST00000374876.4	TSL:1	c.29+1_29+13delGTAAGCCGGGCCG	splice_donor splice_region intron	N/A	ENSP00000364010.4
CCDC40	ENST00000572270.1	TSL:4	n.41_53delGTAAGCCGGGCCG	non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

7.63e-7

AC:

AN:

1310102

Hom.:

AF XY:

0.00

AC XY:

AN XY:

644020

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

27612

American (AMR)

AF:

0.00

AC:

AN:

26818

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

22812

East Asian (EAS)

AF:

0.0000333

AC:

AN:

30070

South Asian (SAS)

AF:

0.00

AC:

AN:

70400

European-Finnish (FIN)

AF:

0.00

AC:

AN:

31796

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5172

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1041274

Other (OTH)

AF:

0.00

AC:

AN:

54148

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

3.3

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over