chr22-38112165-G-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_003560.4(PLA2G6):āc.2417C>Gā(p.Pro806Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000513 in 1,581,658 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P806S) has been classified as Uncertain significance.
Frequency
Consequence
NM_003560.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLA2G6 | NM_003560.4 | c.2417C>G | p.Pro806Arg | missense_variant | 17/17 | ENST00000332509.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLA2G6 | ENST00000332509.8 | c.2417C>G | p.Pro806Arg | missense_variant | 17/17 | 1 | NM_003560.4 | P3 |
Frequencies
GnomAD3 genomes AF: 0.000453 AC: 69AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000856 AC: 169AN: 197464Hom.: 2 AF XY: 0.000783 AC XY: 83AN XY: 106052
GnomAD4 exome AF: 0.000520 AC: 743AN: 1429346Hom.: 3 Cov.: 31 AF XY: 0.000517 AC XY: 366AN XY: 708064
GnomAD4 genome AF: 0.000453 AC: 69AN: 152312Hom.: 0 Cov.: 32 AF XY: 0.000537 AC XY: 40AN XY: 74478
ClinVar
Submissions by phenotype
not provided Benign:5
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2023 | PLA2G6: BS1 - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Dec 03, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 08, 2021 | This variant is associated with the following publications: (PMID: 23182313, 30232368, 30065071, 27942883, 21368765, 21812034, 22213678) - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Autosomal recessive Parkinson disease 14 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Department of Neurology, Xijing Hospital, Fourth Military Medical University | Mar 01, 2022 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 10, 2020 | - - |
Infantile neuroaxonal dystrophy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
PLA2G6-associated neurodegeneration Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 28, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at