22-42168743-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS1
The NM_001378418.1(TCF20):c.5800-7G>A 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 0.0000143 in 1,604,722 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 -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TCF20 | NM_001378418.1 | c.5800-7G>A | 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.5800-7G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NM_001378418.1 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151872Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000126 AC: 3AN: 237870Hom.: 0 AF XY: 0.00000777 AC XY: 1AN XY: 128714
GnomAD4 exome AF: 0.0000145 AC: 21AN: 1452850Hom.: 0 Cov.: 31 AF XY: 0.0000152 AC XY: 11AN XY: 721978
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151872Hom.: 0 Cov.: 31 AF XY: 0.0000270 AC XY: 2AN XY: 74162
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 26, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at