12-9157342-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002864.3(PZP):c.3383G>A(p.Arg1128His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000291 in 1,612,968 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002864.3 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 |
---|---|---|---|---|---|---|---|---|
PZP | NM_002864.3 | c.3383G>A | p.Arg1128His | missense_variant | 28/36 | ENST00000261336.7 | NP_002855.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PZP | ENST00000261336.7 | c.3383G>A | p.Arg1128His | missense_variant | 28/36 | 1 | NM_002864.3 | ENSP00000261336.2 | ||
PZP | ENST00000535230.5 | n.*2852G>A | non_coding_transcript_exon_variant | 25/33 | 1 | ENSP00000440811.1 | ||||
PZP | ENST00000535230.5 | n.*2852G>A | 3_prime_UTR_variant | 25/33 | 1 | ENSP00000440811.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152034Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000361 AC: 9AN: 249270Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134744
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1460816Hom.: 0 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 726700
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152152Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.3383G>A (p.R1128H) alteration is located in exon 28 (coding exon 28) of the PZP gene. This alteration results from a G to A substitution at nucleotide position 3383, causing the arginine (R) at amino acid position 1128 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