rs141575785
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001384732.1(CPLANE1):c.7234-7C>G 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 0.000506 in 1,598,298 control chromosomes in the GnomAD database, including 5 homozygotes. 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 Likely benign (★★).
Frequency
Consequence
NM_001384732.1 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPLANE1 | NM_001384732.1 | c.7234-7C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000651892.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPLANE1 | ENST00000651892.2 | c.7234-7C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NM_001384732.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00260 AC: 395AN: 151976Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.000795 AC: 187AN: 235242Hom.: 0 AF XY: 0.000598 AC XY: 76AN XY: 127056
GnomAD4 exome AF: 0.000286 AC: 413AN: 1446204Hom.: 2 Cov.: 30 AF XY: 0.000238 AC XY: 171AN XY: 718854
GnomAD4 genome ? AF: 0.00260 AC: 395AN: 152094Hom.: 3 Cov.: 32 AF XY: 0.00255 AC XY: 190AN XY: 74366
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | CPLANE1: BP4, BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 22, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
not specified Benign:1
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 22, 2022 | - - |
Joubert syndrome 17 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at