Variant rs7561070 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001349206.2(LPIN1):c.1806+41G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 1,561,184 control chromosomes in the GnomAD database, including 289,607 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.65 ( 34288 hom., cov: 31)

Exomes 𝑓: 0.59 ( 255319 hom. )

Consequence

LPIN1
NM_001349206.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.583

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]

LPIN1 links:

LPIN1 (HGNC:):

LPIN1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BP6

Variant 2-11792047-G-T is Benign according to our data. Variant chr2-11792047-G-T is described in ClinVar as [Benign]. Clinvar id is 262586.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LPIN1	NM_001349206.2 linkuse as main transcript	c.1806+41G>T		intron_variant		ENST00000674199.1	NP_001336135.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LPIN1	ENST00000674199.1 linkuse as main transcript	c.1806+41G>T		intron_variant			NM_001349206.2	ENSP00000501331.1		Q14693-3

Frequencies

GnomAD3 genomes

AF:

0.650

AC:

98665

AN:

151824

Hom.:

34235

Cov.:

show subpopulations

Gnomad AFR

AF:

0.885

Gnomad AMI

AF:

0.580

Gnomad AMR

AF:

0.499

Gnomad ASJ

AF:

0.517

Gnomad EAS

AF:

0.217

Gnomad SAS

AF:

0.422

Gnomad FIN

AF:

0.607

Gnomad MID

AF:

0.535

Gnomad NFE

AF:

0.606

Gnomad OTH

AF:

0.589

GnomAD3 exomes

AF:

0.539

AC:

130096

AN:

241264

Hom.:

38092

AF XY:

0.537

AC XY:

69850

AN XY:

130146

show subpopulations

Gnomad AFR exome

AF:

0.895

Gnomad AMR exome

AF:

0.361

Gnomad ASJ exome

AF:

0.518

Gnomad EAS exome

AF:

0.207

Gnomad SAS exome

AF:

0.429

Gnomad FIN exome

AF:

0.619

Gnomad NFE exome

AF:

0.614

Gnomad OTH exome

AF:

0.545

GnomAD4 exome

AF:

0.593

AC:

835110

AN:

1409238

Hom.:

255319

Cov.:

AF XY:

0.587

AC XY:

412756

AN XY:

703174

show subpopulations

Gnomad4 AFR exome

AF:

0.901

Gnomad4 AMR exome

AF:

0.375

Gnomad4 ASJ exome

AF:

0.515

Gnomad4 EAS exome

AF:

0.236

Gnomad4 SAS exome

AF:

0.440

Gnomad4 FIN exome

AF:

0.622

Gnomad4 NFE exome

AF:

0.619

Gnomad4 OTH exome

AF:

0.570

GnomAD4 genome

AF:

0.650

AC:

98764

AN:

151946

Hom.:

34288

Cov.:

AF XY:

0.641

AC XY:

47607

AN XY:

74290

show subpopulations

Gnomad4 AFR

AF:

0.886

Gnomad4 AMR

AF:

0.499

Gnomad4 ASJ

AF:

0.517

Gnomad4 EAS

AF:

0.217

Gnomad4 SAS

AF:

0.421

Gnomad4 FIN

AF:

0.607

Gnomad4 NFE

AF:

0.606

Gnomad4 OTH

AF:

0.581

Alfa

AF:

0.647

Hom.:

7439

Bravo

AF:

0.651

Asia WGS

AF:

0.331

AC:

1153

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 14, 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. -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.059

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over