chrX-49237077-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_014008.5(CCDC22):c.51-9C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000888 in 112,625 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_014008.5 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC22 | NM_014008.5 | c.51-9C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000376227.4 | |||
CCDC22 | XM_005272599.5 | c.51-9C>T | splice_polypyrimidine_tract_variant, intron_variant | ||||
CCDC22 | XR_430506.4 | n.218-9C>T | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC22 | ENST00000376227.4 | c.51-9C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_014008.5 | P1 | |||
CCDC22 | ENST00000490300.1 | n.185C>T | non_coding_transcript_exon_variant | 1/5 | 3 | ||||
CCDC22 | ENST00000496651.5 | n.192-9C>T | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000888 AC: 1AN: 112625Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34765
GnomAD4 exome Cov.: 30
GnomAD4 genome AF: 0.00000888 AC: 1AN: 112625Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34765
ClinVar
Submissions by phenotype
CCDC22-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 09, 2023 | 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