10-116436746-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001011709.3(PNLIPRP3):c.85A>G(p.Lys29Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,613,292 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PNLIPRP3 | NM_001011709.3 | c.85A>G | p.Lys29Glu | missense_variant | Exon 2 of 12 | ENST00000369230.4 | NP_001011709.2 | |
PNLIPRP3 | XM_011539276.2 | c.85A>G | p.Lys29Glu | missense_variant | Exon 2 of 10 | XP_011537578.1 | ||
PNLIPRP3 | XM_011539279.2 | c.-111-6309A>G | intron_variant | Intron 1 of 10 | XP_011537581.1 | |||
PNLIPRP3 | XM_011539278.1 | c.-362A>G | upstream_gene_variant | XP_011537580.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152188Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000359 AC: 9AN: 250686Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135460
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1460986Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 726782
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152306Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.85A>G (p.K29E) alteration is located in exon 2 (coding exon 2) of the PNLIPRP3 gene. This alteration results from a A to G substitution at nucleotide position 85, causing the lysine (K) at amino acid position 29 to be replaced by a glutamic acid (E). 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