6-42923128-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_138296.3(PTCRA):c.160C>T(p.Pro54Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000768 in 1,614,100 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_138296.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTCRA | ENST00000304672.6 | c.160C>T | p.Pro54Ser | missense_variant | Exon 2 of 4 | 1 | NM_138296.3 | ENSP00000304447.2 | ||
PTCRA | ENST00000441198.4 | c.102-17C>T | intron_variant | Intron 2 of 4 | 1 | ENSP00000409550.1 | ||||
PTCRA | ENST00000446507.5 | c.59-1101C>T | intron_variant | Intron 1 of 2 | 1 | ENSP00000392288.1 | ||||
PTCRA | ENST00000616441.2 | c.160C>T | p.Pro54Ser | missense_variant | Exon 2 of 4 | 2 | ENSP00000477815.1 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152224Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251394Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135886
GnomAD4 exome AF: 0.0000814 AC: 119AN: 1461876Hom.: 0 Cov.: 32 AF XY: 0.0000729 AC XY: 53AN XY: 727240
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152224Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.160C>T (p.P54S) alteration is located in exon 2 (coding exon 2) of the PTCRA gene. This alteration results from a C to T substitution at nucleotide position 160, causing the proline (P) at amino acid position 54 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