chr22-43923962-C-T
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_025225.3(PNPLA3):c.51C>T(p.Phe17=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PNPLA3
NM_025225.3 synonymous
NM_025225.3 synonymous
Scores
1
1
Clinical Significance
Conservation
PhyloP100: 0.888
Genes affected
PNPLA3 (HGNC:18590): (patatin like phospholipase domain containing 3) The protein encoded by this gene is a triacylglycerol lipase that mediates triacylglycerol hydrolysis in adipocytes. The encoded protein, which appears to be membrane bound, may be involved in the balance of energy usage/storage in adipocytes. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP6
Variant 22-43923962-C-T is Benign according to our data. Variant chr22-43923962-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2653272.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.888 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PNPLA3 | NM_025225.3 | c.51C>T | p.Phe17= | synonymous_variant | 1/9 | ENST00000216180.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PNPLA3 | ENST00000216180.8 | c.51C>T | p.Phe17= | synonymous_variant | 1/9 | 1 | NM_025225.3 | P1 | |
PNPLA3 | ENST00000423180.2 | c.51C>T | p.Phe17= | synonymous_variant | 1/9 | 2 | |||
PNPLA3 | ENST00000406117.6 | c.51C>T | p.Phe17= | synonymous_variant, NMD_transcript_variant | 1/10 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1432484Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 712904
GnomAD4 exome
Data not reliable, filtered out with message: AC0
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1432484
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31
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0
AN XY:
712904
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
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32
Bravo
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2022 | PNPLA3: PM2:Supporting, BP4, BP7 - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at