chr22-42168695-G-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_001378418.1(TCF20):c.5841C>G(p.Thr1947=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000224 in 1,610,968 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T1947T) has been classified as Likely benign.
Frequency
Consequence
NM_001378418.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TCF20 | NM_001378418.1 | c.5841C>G | p.Thr1947= | synonymous_variant | 5/6 | ENST00000677622.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCF20 | ENST00000677622.1 | c.5841C>G | p.Thr1947= | synonymous_variant | 5/6 | NM_001378418.1 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000592 AC: 9AN: 152088Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000615 AC: 15AN: 244030Hom.: 0 AF XY: 0.0000530 AC XY: 7AN XY: 132178
GnomAD4 exome AF: 0.000241 AC: 352AN: 1458762Hom.: 0 Cov.: 31 AF XY: 0.000233 AC XY: 169AN XY: 725504
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152206Hom.: 0 Cov.: 31 AF XY: 0.0000403 AC XY: 3AN XY: 74434
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at