rs762961824
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_017950.4(CCDC40):c.677-8C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,609,598 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_017950.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC40 | NM_017950.4 | c.677-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000397545.9 | |||
CCDC40 | NM_001243342.2 | c.677-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
CCDC40 | NM_001330508.2 | c.677-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC40 | ENST00000397545.9 | c.677-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_017950.4 | P2 | |||
ENST00000695611.1 | n.1432-1056G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000244 AC: 6AN: 245774Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 133816
GnomAD4 exome AF: 0.0000206 AC: 30AN: 1457474Hom.: 0 Cov.: 30 AF XY: 0.0000152 AC XY: 11AN XY: 725168
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74302
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Dec 15, 2017 | c.677-8C>T in intron 4 of CCDC40: This variant is not expected to have clinical significance because it is not located within the conserved splice consensus seq uence. It has been identified in 0.12%(4/33486) of Latino chromosomes by the Gen ome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs7629 61824). - |
Primary ciliary dyskinesia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 13, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at