chr22-42168744-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001378418.1(TCF20):c.5800-8C>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 0.0000829 in 1,605,240 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_001378418.1 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 |
---|---|---|---|---|---|---|---|
TCF20 | NM_001378418.1 | c.5800-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000677622.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCF20 | ENST00000677622.1 | c.5800-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NM_001378418.1 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000362 AC: 55AN: 152012Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000882 AC: 21AN: 238044Hom.: 0 AF XY: 0.0000854 AC XY: 11AN XY: 128856
GnomAD4 exome AF: 0.0000530 AC: 77AN: 1453110Hom.: 0 Cov.: 31 AF XY: 0.0000499 AC XY: 36AN XY: 722148
GnomAD4 genome ? AF: 0.000368 AC: 56AN: 152130Hom.: 0 Cov.: 31 AF XY: 0.000336 AC XY: 25AN XY: 74356
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2023 | TCF20: BP4, BS1 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
TCF20-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 26, 2024 | 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