rs150190277
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_003560.4(PLA2G6):āc.495G>Cā(p.Gly165=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000722 in 1,614,166 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. G165G) has been classified as Likely benign.
Frequency
Consequence
NM_003560.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLA2G6 | NM_003560.4 | c.495G>C | p.Gly165= | synonymous_variant | 4/17 | ENST00000332509.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLA2G6 | ENST00000332509.8 | c.495G>C | p.Gly165= | synonymous_variant | 4/17 | 1 | NM_003560.4 | P3 | |
ENST00000624072.1 | n.13004C>G | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.00352 AC: 536AN: 152186Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.000927 AC: 233AN: 251466Hom.: 1 AF XY: 0.000677 AC XY: 92AN XY: 135914
GnomAD4 exome AF: 0.000428 AC: 625AN: 1461862Hom.: 3 Cov.: 33 AF XY: 0.000371 AC XY: 270AN XY: 727234
GnomAD4 genome ? AF: 0.00355 AC: 540AN: 152304Hom.: 3 Cov.: 32 AF XY: 0.00328 AC XY: 244AN XY: 74476
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2023 | PLA2G6: BP4, BP7, BS1, BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 06, 2021 | - - |
Iron accumulation in brain Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 08, 2013 | - - |
Infantile neuroaxonal dystrophy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at