rs141043192
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 2P and 17B. PM2BP4_StrongBP6_Very_StrongBP7BS1
The NM_001375808.2(LPIN2):c.2583C>T(p.Phe861=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000979 in 1,613,942 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00053 ( 1 hom., cov: 32)
Exomes 𝑓: 0.000053 ( 0 hom. )
Consequence
LPIN2
NM_001375808.2 synonymous
NM_001375808.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.05
Genes affected
LPIN2 (HGNC:14450): (lipin 2) Mouse studies suggest that this gene functions during normal adipose tissue development and may play a role in human triglyceride metabolism. This gene represents a candidate gene for human lipodystrophy, characterized by loss of body fat, fatty liver, hypertriglyceridemia, and insulin resistance. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
?
Variant 18-2920401-G-A is Benign according to our data. Variant chr18-2920401-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 536356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=1.05 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000525 (80/152334) while in subpopulation AFR AF= 0.00188 (78/41572). AF 95% confidence interval is 0.00154. There are 1 homozygotes in gnomad4. There are 39 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LPIN2 | NM_001375808.2 | c.2583C>T | p.Phe861= | synonymous_variant | 20/20 | ENST00000677752.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LPIN2 | ENST00000677752.1 | c.2583C>T | p.Phe861= | synonymous_variant | 20/20 | NM_001375808.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000526 AC: 80AN: 152216Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000112 AC: 28AN: 251056Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135868
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GnomAD4 exome AF: 0.0000534 AC: 78AN: 1461608Hom.: 0 Cov.: 33 AF XY: 0.0000440 AC XY: 32AN XY: 727118
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GnomAD4 genome ? AF: 0.000525 AC: 80AN: 152334Hom.: 1 Cov.: 32 AF XY: 0.000524 AC XY: 39AN XY: 74496
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ClinVar
Significance: Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Majeed syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
LPIN2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 04, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Autoinflammatory syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Oct 01, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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