17-80081797-C-T
Variant summary
Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_017950.4(CCDC40):c.1806+8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000212 in 1,613,890 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_017950.4 splice_region, intron
Scores
Clinical Significance
Conservation
Publications
- primary ciliary dyskinesia 15Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, ClinGen, Ambry Genetics, Labcorp Genetics (formerly Invitae), PanelApp Australia, Laboratory for Molecular Medicine
- primary ciliary dyskinesiaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- autoimmune diseaseInheritance: AR Classification: LIMITED Submitted by: Ambry Genetics
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ACMG classification
Our verdict: Likely_benign. The variant received -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCDC40 | NM_017950.4 | c.1806+8C>T | splice_region_variant, intron_variant | Intron 11 of 19 | ENST00000397545.9 | NP_060420.2 | ||
CCDC40 | NM_001243342.2 | c.1806+8C>T | splice_region_variant, intron_variant | Intron 11 of 17 | NP_001230271.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC40 | ENST00000397545.9 | c.1806+8C>T | splice_region_variant, intron_variant | Intron 11 of 19 | 5 | NM_017950.4 | ENSP00000380679.4 | |||
CCDC40 | ENST00000574799.5 | n.1343+8C>T | splice_region_variant, intron_variant | Intron 7 of 15 | 1 | |||||
CCDC40 | ENST00000572253.5 | n.355C>T | non_coding_transcript_exon_variant | Exon 1 of 6 | 2 | |||||
CCDC40 | ENST00000374877.7 | c.1806+8C>T | splice_region_variant, intron_variant | Intron 11 of 17 | 5 | ENSP00000364011.3 |
Frequencies
GnomAD3 genomes AF: 0.000677 AC: 103AN: 152188Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.000202 AC: 50AN: 247810 AF XY: 0.000193 show subpopulations
GnomAD4 exome AF: 0.000164 AC: 239AN: 1461584Hom.: 0 Cov.: 31 AF XY: 0.000165 AC XY: 120AN XY: 727100 show subpopulations
GnomAD4 genome AF: 0.000676 AC: 103AN: 152306Hom.: 0 Cov.: 33 AF XY: 0.000631 AC XY: 47AN XY: 74464 show subpopulations
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:1
- -
CCDC40-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at