chr11-18306240-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP3_ModeratePP5
The NM_181507.2(HPS5):c.719G>C(p.Arg240Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,613,756 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 Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R240C) has been classified as Uncertain significance.
Frequency
Consequence
NM_181507.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HPS5 | NM_181507.2 | c.719G>C | p.Arg240Pro | missense_variant | 7/23 | ENST00000349215.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HPS5 | ENST00000349215.8 | c.719G>C | p.Arg240Pro | missense_variant | 7/23 | 1 | NM_181507.2 | P1 | |
HPS5 | ENST00000396253.7 | c.377G>C | p.Arg126Pro | missense_variant | 6/22 | 1 | |||
HPS5 | ENST00000438420.6 | c.377G>C | p.Arg126Pro | missense_variant | 6/22 | 1 | |||
HPS5 | ENST00000531848.1 | c.377G>C | p.Arg126Pro | missense_variant | 6/11 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251474Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135912
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461642Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 727150
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152114Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74300
ClinVar
Submissions by phenotype
Hermansky-Pudlak syndrome 5 Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Laboratoire de Génétique Moléculaire, CHU Bordeaux | Mar 14, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at