chr4-106046684-GA-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP6_Very_Strong
The NM_001163435.3(TBCK):c.2572-5del 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 0.000131 in 1,368,876 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001163435.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBCK | NM_001163435.3 | c.2572-5del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000394708.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBCK | ENST00000394708.7 | c.2572-5del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001163435.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 149910Hom.: 0 Cov.: 32 FAILED QC
GnomAD4 exome AF: 0.000131 AC: 179AN: 1368876Hom.: 0 Cov.: 22 AF XY: 0.000121 AC XY: 83AN XY: 683856
GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 149910Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73076
ClinVar
Submissions by phenotype
TBCK-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 09, 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). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 16, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at