chr17-59676949-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_004859.4(CLTC):c.2562-5C>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 0.000163 in 1,604,054 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 Likely benign (★★).
Frequency
Consequence
NM_004859.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLTC | NM_004859.4 | c.2562-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000269122.8 | |||
CLTC | NM_001288653.2 | c.2574-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLTC | ENST00000269122.8 | c.2562-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004859.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000171 AC: 26AN: 151684Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.000162 AC: 235AN: 1452252Hom.: 0 Cov.: 31 AF XY: 0.000158 AC XY: 114AN XY: 722888
GnomAD4 genome ? AF: 0.000171 AC: 26AN: 151802Hom.: 0 Cov.: 32 AF XY: 0.000162 AC XY: 12AN XY: 74160
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | CLTC: BP4 - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
CLTC-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 17, 2019 | 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