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rs2278513

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001349206.2(LPIN1):c.830+1586T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 152,156 control chromosomes in the GnomAD database, including 15,006 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.42 ( 15006 hom., cov: 33)

Consequence

LPIN1
NM_001349206.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.07
Variant links:
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LPIN1NM_001349206.2 linkuse as main transcriptc.830+1586T>C intron_variant ENST00000674199.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LPIN1ENST00000674199.1 linkuse as main transcriptc.830+1586T>C intron_variant NM_001349206.2 P4Q14693-3

Frequencies

GnomAD3 genomes
AF:
0.419
AC:
63698
AN:
152038
Hom.:
15014
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.224
Gnomad AMI
AF:
0.389
Gnomad AMR
AF:
0.405
Gnomad ASJ
AF:
0.434
Gnomad EAS
AF:
0.215
Gnomad SAS
AF:
0.338
Gnomad FIN
AF:
0.504
Gnomad MID
AF:
0.551
Gnomad NFE
AF:
0.547
Gnomad OTH
AF:
0.441
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.419
AC:
63702
AN:
152156
Hom.:
15006
Cov.:
33
AF XY:
0.415
AC XY:
30873
AN XY:
74390
show subpopulations
Gnomad4 AFR
AF:
0.224
Gnomad4 AMR
AF:
0.405
Gnomad4 ASJ
AF:
0.434
Gnomad4 EAS
AF:
0.216
Gnomad4 SAS
AF:
0.338
Gnomad4 FIN
AF:
0.504
Gnomad4 NFE
AF:
0.547
Gnomad4 OTH
AF:
0.437
Alfa
AF:
0.506
Hom.:
20411
Bravo
AF:
0.399
Asia WGS
AF:
0.236
AC:
821
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
Cadd
Benign
0.91
Dann
Benign
0.35

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2278513; hg19: chr2-11917905; API