rs886038654
Positions:
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP6_Very_StrongBP7
The NM_020376.4(PNPLA2):c.1458_1459delinsTC(p.ProLeu486=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P486P) has been classified as Benign.
Frequency
Genomes: not found (cov: 33)
Consequence
PNPLA2
NM_020376.4 synonymous
NM_020376.4 synonymous
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.511
Genes affected
PNPLA2 (HGNC:30802): (patatin like phospholipase domain containing 2) This gene encodes an enzyme which catalyzes the first step in the hydrolysis of triglycerides in adipose tissue. Mutations in this gene are associated with neutral lipid storage disease with myopathy. [provided by RefSeq, Jul 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP6
?
Variant 11-824805-CT-TC is Benign according to our data. Variant chr11-824805-CT-TC is described in ClinVar as [Likely_benign]. Clinvar id is 261237.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.511 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PNPLA2 | NM_020376.4 | c.1458_1459delinsTC | p.ProLeu486= | synonymous_variant | 10/10 | ENST00000336615.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PNPLA2 | ENST00000336615.9 | c.1458_1459delinsTC | p.ProLeu486= | synonymous_variant | 10/10 | 1 | NM_020376.4 | P1 | |
PNPLA2 | ENST00000529255.1 | n.888_889delinsTC | non_coding_transcript_exon_variant | 4/4 | 1 | ||||
ENST00000532946.1 | n.307-943_307-942delinsGA | intron_variant, non_coding_transcript_variant | 5 | ||||||
PNPLA2 | ENST00000525250.5 | n.2312_2313delinsTC | non_coding_transcript_exon_variant | 6/6 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Neutral lipid storage myopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 05, 2023 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at