16-14672746-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_003561.3(PLA2G10):c.359C>T(p.Pro120Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000149 in 1,613,584 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. P120P) has been classified as Likely benign.
Frequency
Consequence
NM_003561.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLA2G10 | NM_003561.3 | c.359C>T | p.Pro120Leu | missense_variant | 4/4 | ENST00000438167.8 | |
PLA2G10 | XM_047434757.1 | c.359C>T | p.Pro120Leu | missense_variant | 5/5 | ||
PLA2G10 | NR_133651.1 | n.819C>T | non_coding_transcript_exon_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLA2G10 | ENST00000438167.8 | c.359C>T | p.Pro120Leu | missense_variant | 4/4 | 1 | NM_003561.3 | P1 | |
PLA2G10 | ENST00000567462.1 | c.*82C>T | 3_prime_UTR_variant, NMD_transcript_variant | 5/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152038Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251186Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135756
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461546Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727092
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152038Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74246
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 17, 2023 | The c.359C>T (p.P120L) alteration is located in exon 4 (coding exon 4) of the PLA2G10 gene. This alteration results from a C to T substitution at nucleotide position 359, causing the proline (P) at amino acid position 120 to be replaced by a leucine (L). 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