12-6828736-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014262.5(P3H3):c.296C>A(p.Pro99His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000393 in 1,246,350 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014262.5 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 |
---|---|---|---|---|---|---|---|
P3H3 | NM_014262.5 | c.296C>A | p.Pro99His | missense_variant | 1/15 | ENST00000290510.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
P3H3 | ENST00000290510.10 | c.296C>A | p.Pro99His | missense_variant | 1/15 | 1 | NM_014262.5 | P1 | |
GPR162 | ENST00000545321.1 | c.570-1123C>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000461 AC: 7AN: 151772Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.0000384 AC: 42AN: 1094470Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 21AN XY: 520086
GnomAD4 genome ? AF: 0.0000461 AC: 7AN: 151880Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74248
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 27, 2022 | The c.296C>A (p.P99H) alteration is located in exon 1 (coding exon 1) of the P3H3 gene. This alteration results from a C to A substitution at nucleotide position 296, causing the proline (P) at amino acid position 99 to be replaced by a histidine (H). 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