chr22-42168712-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001378418.1(TCF20):āc.5824C>Gā(p.Pro1942Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000387 in 1,611,374 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P1942H) has been classified as Benign.
Frequency
Consequence
NM_001378418.1 missense
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.5824C>G | p.Pro1942Ala | missense_variant | 5/6 | ENST00000677622.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCF20 | ENST00000677622.1 | c.5824C>G | p.Pro1942Ala | missense_variant | 5/6 | NM_001378418.1 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000460 AC: 70AN: 152164Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000445 AC: 109AN: 244782Hom.: 2 AF XY: 0.000445 AC XY: 59AN XY: 132636
GnomAD4 exome AF: 0.000380 AC: 554AN: 1459092Hom.: 2 Cov.: 31 AF XY: 0.000357 AC XY: 259AN XY: 725698
GnomAD4 genome AF: 0.000460 AC: 70AN: 152282Hom.: 0 Cov.: 31 AF XY: 0.000336 AC XY: 25AN XY: 74450
ClinVar
Submissions by phenotype
TCF20-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 19, 2022 | 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 | Jan 21, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at