10-116444457-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001011709.3(PNLIPRP3):c.400G>C(p.Val134Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000156 in 1,613,350 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PNLIPRP3 | NM_001011709.3 | c.400G>C | p.Val134Leu | missense_variant | 4/12 | ENST00000369230.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PNLIPRP3 | ENST00000369230.4 | c.400G>C | p.Val134Leu | missense_variant | 4/12 | 1 | NM_001011709.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000164 AC: 25AN: 152130Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000163 AC: 41AN: 251404Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135868
GnomAD4 exome AF: 0.000155 AC: 226AN: 1461102Hom.: 0 Cov.: 30 AF XY: 0.000158 AC XY: 115AN XY: 726872
GnomAD4 genome ? AF: 0.000164 AC: 25AN: 152248Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74448
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2022 | The c.400G>C (p.V134L) alteration is located in exon 4 (coding exon 4) of the PNLIPRP3 gene. This alteration results from a G to C substitution at nucleotide position 400, causing the valine (V) at amino acid position 134 to be replaced by a leucine (L). 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