2-11713862-A-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001261428.3(LPIN1):c.138+50A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 1,292,316 control chromosomes in the GnomAD database, including 170,807 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.40 ( 14148 hom., cov: 33)
Exomes 𝑓: 0.52 ( 156659 hom. )
Consequence
LPIN1
NM_001261428.3 intron
NM_001261428.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0360
Genes affected
LPIN1 (HGNC:13345): (lipin 1) This gene encodes a magnesium-ion-dependent phosphatidic acid phosphohydrolase enzyme that catalyzes the penultimate step in triglyceride synthesis including the dephosphorylation of phosphatidic acid to yield diacylglycerol. Expression of this gene is required for adipocyte differentiation and it also functions as a nuclear transcriptional coactivator with some peroxisome proliferator-activated receptors to modulate expression of other genes involved in lipid metabolism. Mutations in this gene are associated with metabolic syndrome, type 2 diabetes, acute recurrent rhabdomyolysis, and autosomal recessive acute recurrent myoglobinuria (ARARM). This gene is also a candidate for several human lipodystrophy syndromes. [provided by RefSeq, Mar 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 2-11713862-A-T is Benign according to our data. Variant chr2-11713862-A-T is described in ClinVar as [Benign]. Clinvar id is 683084.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LPIN1 | NM_001261428.3 | c.138+50A>T | intron_variant | ||||
LPIN1 | NM_001349207.2 | c.81+36134A>T | intron_variant | ||||
LPIN1 | NM_001349208.2 | c.138+50A>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LPIN1 | ENST00000449576.6 | c.138+50A>T | intron_variant | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.397 AC: 60323AN: 152042Hom.: 14147 Cov.: 33
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GnomAD3 exomes AF: 0.494 AC: 60640AN: 122656Hom.: 15538 AF XY: 0.504 AC XY: 33783AN XY: 67052
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GnomAD4 exome AF: 0.522 AC: 594804AN: 1140156Hom.: 156659 Cov.: 15 AF XY: 0.524 AC XY: 299669AN XY: 572216
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GnomAD4 genome ? AF: 0.396 AC: 60330AN: 152160Hom.: 14148 Cov.: 33 AF XY: 0.400 AC XY: 29718AN XY: 74376
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 16, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
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Name
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at