6-35140756-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001370687.1(TCP11):c.115C>A(p.Pro39Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000471 in 1,527,594 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001370687.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TCP11 | NM_001370687.1 | c.115C>A | p.Pro39Thr | missense_variant | 2/10 | ENST00000311875.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCP11 | ENST00000311875.11 | c.115C>A | p.Pro39Thr | missense_variant | 2/10 | 1 | NM_001370687.1 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152062Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000172 AC: 3AN: 174344Hom.: 0 AF XY: 0.0000108 AC XY: 1AN XY: 92968
GnomAD4 exome AF: 0.0000487 AC: 67AN: 1375532Hom.: 0 Cov.: 30 AF XY: 0.0000576 AC XY: 39AN XY: 676726
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152062Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74268
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2022 | The c.154C>A (p.P52T) alteration is located in exon 2 (coding exon 2) of the TCP11 gene. This alteration results from a C to A substitution at nucleotide position 154, causing the proline (P) at amino acid position 52 to be replaced by a threonine (T). 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