chr22-42168712-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001378418.1(TCF20):c.5824C>T(p.Pro1942Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000372 in 1,611,378 control chromosomes in the GnomAD database, including 4 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 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.5824C>T | p.Pro1942Ser | missense_variant | 5/6 | ENST00000677622.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCF20 | ENST00000677622.1 | c.5824C>T | p.Pro1942Ser | missense_variant | 5/6 | NM_001378418.1 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00172 AC: 261AN: 152162Hom.: 2 Cov.: 31
GnomAD3 exomes AF: 0.000515 AC: 126AN: 244782Hom.: 2 AF XY: 0.000377 AC XY: 50AN XY: 132636
GnomAD4 exome AF: 0.000232 AC: 339AN: 1459098Hom.: 2 Cov.: 31 AF XY: 0.000223 AC XY: 162AN XY: 725702
GnomAD4 genome AF: 0.00171 AC: 261AN: 152280Hom.: 2 Cov.: 31 AF XY: 0.00168 AC XY: 125AN XY: 74448
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at