10-116476659-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001011709.3(PNLIPRP3):c.1180C>T(p.Leu394Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000383 in 1,566,862 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001011709.3 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 |
---|---|---|---|---|---|---|---|
PNLIPRP3 | NM_001011709.3 | c.1180C>T | p.Leu394Phe | missense_variant | 11/12 | ENST00000369230.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PNLIPRP3 | ENST00000369230.4 | c.1180C>T | p.Leu394Phe | missense_variant | 11/12 | 1 | NM_001011709.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000190 AC: 4AN: 210418Hom.: 0 AF XY: 0.00000875 AC XY: 1AN XY: 114334
GnomAD4 exome AF: 0.00000283 AC: 4AN: 1414668Hom.: 0 Cov.: 30 AF XY: 0.00000142 AC XY: 1AN XY: 701780
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 12, 2023 | The c.1180C>T (p.L394F) alteration is located in exon 11 (coding exon 11) of the PNLIPRP3 gene. This alteration results from a C to T substitution at nucleotide position 1180, causing the leucine (L) at amino acid position 394 to be replaced by a phenylalanine (F). 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