10-116630009-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The ENST00000579578.6(PNLIPRP2):c.644C>T(p.Ala215Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000096 in 1,459,028 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000579578.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PNLIPRP2 | NR_103727.2 | n.670C>T | non_coding_transcript_exon_variant | Exon 7 of 13 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000408 AC: 1AN: 245082Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132704
GnomAD4 exome AF: 0.00000960 AC: 14AN: 1459028Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 725388
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.647C>T (p.A216V) alteration is located in exon 7 (coding exon 7) of the PNLIPRP2 gene. This alteration results from a C to T substitution at nucleotide position 647, causing the alanine (A) at amino acid position 216 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