2-11713648-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001261428.3(LPIN1):c.82-108T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 626,790 control chromosomes in the GnomAD database, including 75,944 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.40 (14153 hom., cov: 33)
  • Exomes 𝑓: 0.50 (61791 hom.)
• Consequence: LPIN1 NM_001261428.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.26

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BP6: Variant 2-11713648-T-C is Benign according to our data. Variant chr2-11713648-T-C is described in ClinVar as [Benign]. Clinvar id is 683083.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LPIN1	NM_001261428.3	c.82-108T>C		intron_variant
LPIN1	NM_001349207.2	c.81+35920T>C		intron_variant
LPIN1	NM_001349208.2	c.82-108T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LPIN1	ENST00000449576.6	c.82-108T>C		intron_variant		2		A2

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60321 AN: 151992 Hom.: 14152 Cov.: 33

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.439

GnomAD4 exome AF: 0.503 AC: 238604 AN: 474680 Hom.: 61791 AF XY: 0.509 AC XY: 127401 AN XY: 250366

Gnomad4 AFR exome AF: 0.127

Gnomad4 AMR exome AF: 0.518

Gnomad4 ASJ exome AF: 0.542

Gnomad4 EAS exome AF: 0.434

Gnomad4 SAS exome AF: 0.581

Gnomad4 FIN exome AF: 0.499

Gnomad4 NFE exome AF: 0.515

Gnomad4 OTH exome AF: 0.482

GnomAD4 genome AF: 0.397 AC: 60328 AN: 152110 Hom.: 14153 Cov.: 33 AF XY: 0.400 AC XY: 29731 AN XY: 74354

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.429

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.442

Alfa AF: 0.434 Hom.: 1985

Bravo AF: 0.380

Asia WGS AF: 0.507 AC: 1761 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

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

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.15
Dann	Benign	0.36

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12465629; hg19: chr2-11853774;