chr22-42168711-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001378418.1(TCF20):c.5825C>G(p.Pro1942Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000844 in 1,611,334 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P1942A) has been classified as Likely benign.
Frequency
Consequence
NM_001378418.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TCF20 | NM_001378418.1 | c.5825C>G | p.Pro1942Arg | missense_variant | 5/6 | ENST00000677622.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCF20 | ENST00000677622.1 | c.5825C>G | p.Pro1942Arg | missense_variant | 5/6 | NM_001378418.1 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000131 AC: 20AN: 152142Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000904 AC: 22AN: 243466Hom.: 0 AF XY: 0.0000985 AC XY: 13AN XY: 131946
GnomAD4 exome AF: 0.0000788 AC: 115AN: 1459074Hom.: 0 Cov.: 31 AF XY: 0.0000785 AC XY: 57AN XY: 725658
GnomAD4 genome ? AF: 0.000138 AC: 21AN: 152260Hom.: 0 Cov.: 31 AF XY: 0.0000940 AC XY: 7AN XY: 74452
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 20, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at