20-610039-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004609.4(TCF15):c.199C>T(p.Pro67Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000109 in 1,188,320 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004609.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TCF15 | NM_004609.4 | c.199C>T | p.Pro67Ser | missense_variant | 1/2 | ENST00000246080.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCF15 | ENST00000246080.4 | c.199C>T | p.Pro67Ser | missense_variant | 1/2 | 1 | NM_004609.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000818 AC: 12AN: 146720Hom.: 0 Cov.: 32
GnomAD4 exome AF: 9.60e-7 AC: 1AN: 1041600Hom.: 0 Cov.: 46 AF XY: 0.00000203 AC XY: 1AN XY: 493560
GnomAD4 genome AF: 0.0000818 AC: 12AN: 146720Hom.: 0 Cov.: 32 AF XY: 0.0000280 AC XY: 2AN XY: 71412
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 01, 2022 | The c.199C>T (p.P67S) alteration is located in exon 1 (coding exon 1) of the TCF15 gene. This alteration results from a C to T substitution at nucleotide position 199, causing the proline (P) at amino acid position 67 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at