9-129665931-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_016307.4(PRRX2):āc.64C>Gā(p.Pro22Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0005 in 1,121,662 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 (ā ).
Frequency
Consequence
NM_016307.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRRX2 | NM_016307.4 | c.64C>G | p.Pro22Ala | missense_variant | 1/4 | ENST00000372469.6 | NP_057391.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000285 AC: 42AN: 147282Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000664 AC: 1AN: 15066Hom.: 0 AF XY: 0.000109 AC XY: 1AN XY: 9186
GnomAD4 exome AF: 0.000533 AC: 519AN: 974274Hom.: 0 Cov.: 29 AF XY: 0.000496 AC XY: 234AN XY: 471370
GnomAD4 genome AF: 0.000285 AC: 42AN: 147388Hom.: 0 Cov.: 31 AF XY: 0.000320 AC XY: 23AN XY: 71786
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2021 | The c.64C>G (p.P22A) alteration is located in exon 1 (coding exon 1) of the PRRX2 gene. This alteration results from a C to G substitution at nucleotide position 64, causing the proline (P) at amino acid position 22 to be replaced by an alanine (A). 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