12-9160461-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002864.3(PZP):c.2902A>G(p.Ile968Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,613,728 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I968T) has been classified 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 | UniProt |
---|---|---|---|---|---|---|---|
PZP | NM_002864.3 | c.2902A>G | p.Ile968Val | missense_variant | 24/36 | ENST00000261336.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PZP | ENST00000261336.7 | c.2902A>G | p.Ile968Val | missense_variant | 24/36 | 1 | NM_002864.3 | P1 | |
PZP | ENST00000535230.5 | c.*2371A>G | 3_prime_UTR_variant, NMD_transcript_variant | 21/33 | 1 | ||||
PZP | ENST00000539983.5 | n.1476A>G | non_coding_transcript_exon_variant | 9/9 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152220Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461508Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 727062
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 20, 2023 | The c.2902A>G (p.I968V) alteration is located in exon 24 (coding exon 24) of the PZP gene. This alteration results from a A to G substitution at nucleotide position 2902, causing the isoleucine (I) at amino acid position 968 to be replaced by a valine (V). 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