rs6082

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000236.3(LIPC):c.591A>G(p.Gly197Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.098 in 1,613,402 control chromosomes in the GnomAD database, including 11,312 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 1148 hom., cov: 34)

Exomes 𝑓: 0.097 ( 10164 hom. )

Consequence

LIPC
NM_000236.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -2.09

Publications

22 publications found

Variant links:

Genes affected

LIPC (HGNC:6619): (lipase C, hepatic type) Enables phospholipase A1 activity and triglyceride lipase activity. Involved in several processes, including lipid homeostasis; plasma lipoprotein particle remodeling; and triglyceride catabolic process. Located in extracellular space. Implicated in several diseases, including Alzheimer's disease; coronary artery disease; familial combined hyperlipidemia; peripheral vascular disease; and type 2 diabetes mellitus. Biomarker of hyperinsulinism; obesity; and type 1 diabetes mellitus. [provided by Alliance of Genome Resources, Apr 2022]

LIPC Gene-Disease associations (from GenCC):

hyperlipidemia due to hepatic triglyceride lipase deficiency
Inheritance: AR, Unknown Classification: STRONG, LIMITED Submitted by: Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae), Ambry Genetics

LIPC links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 15-58545758-A-G is Benign according to our data. Variant chr15-58545758-A-G is described in ClinVar as Benign. ClinVar VariationId is 316664.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.09 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LIPC	NM_000236.3 link	c.591A>G	p.Gly197Gly	synonymous_variant	Exon 5 of 9	ENST00000299022.10	NP_000227.2	P11150A6H8L5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIPC	ENST00000299022.10 link	c.591A>G	p.Gly197Gly	synonymous_variant	Exon 5 of 9	1	NM_000236.3	ENSP00000299022.5		P11150

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15825

AN:

151996

Hom.:

1148

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0914

Gnomad AMI

AF:

0.0198

Gnomad AMR

AF:

0.152

Gnomad ASJ

AF:

0.0804

Gnomad EAS

AF:

0.415

Gnomad SAS

AF:

0.121

Gnomad FIN

AF:

0.109

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.0781

Gnomad OTH

AF:

0.103

GnomAD2 exomes

AF:

0.128

AC:

32071

AN:

251258

AF XY:

0.121

show subpopulations

Gnomad AFR exome

AF:

0.0918

Gnomad AMR exome

AF:

0.207

Gnomad ASJ exome

AF:

0.0790

Gnomad EAS exome

AF:

0.418

Gnomad FIN exome

AF:

0.106

Gnomad NFE exome

AF:

0.0781

Gnomad OTH exome

AF:

0.0971

GnomAD4 exome

AF:

0.0974

AC:

142273

AN:

1461288

Hom.:

10164

Cov.:

AF XY:

0.0966

AC XY:

70260

AN XY:

727006

show subpopulations

African (AFR)

AF:

0.0883

AC:

2957

AN:

33472

American (AMR)

AF:

0.201

AC:

8987

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.0818

AC:

2138

AN:

26132

East Asian (EAS)

AF:

0.441

AC:

17495

AN:

39694

South Asian (SAS)

AF:

0.105

AC:

9048

AN:

86250

European-Finnish (FIN)

AF:

0.109

AC:

5833

AN:

53398

Middle Eastern (MID)

AF:

0.0650

AC:

374

AN:

5758

European-Non Finnish (NFE)

AF:

0.0800

AC:

88922

AN:

1111484

Other (OTH)

AF:

0.108

AC:

6519

AN:

60378

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

6304

12609

18913

25218

31522

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3628

7256

10884

14512

18140

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.104

AC:

15840

AN:

152114

Hom.:

1148

Cov.:

AF XY:

0.108

AC XY:

8030

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.0913

AC:

3791

AN:

41510

American (AMR)

AF:

0.151

AC:

2315

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0804

AC:

279

AN:

3470

East Asian (EAS)

AF:

0.416

AC:

2145

AN:

5158

South Asian (SAS)

AF:

0.121

AC:

582

AN:

4804

European-Finnish (FIN)

AF:

0.109

AC:

1155

AN:

10576

Middle Eastern (MID)

AF:

0.0748

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0781

AC:

5308

AN:

67998

Other (OTH)

AF:

0.107

AC:

225

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

725

1450

2175

2900

3625

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

184

368

552

736

920

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0849

Hom.:

1451

Bravo

AF:

0.112

Asia WGS

AF:

0.271

AC:

941

AN:

3478

EpiCase

AF:

0.0766

EpiControl

AF:

0.0719

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Aug 30, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Hyperlipidemia due to hepatic triglyceride lipase deficiency

Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.4

(source)

DANN

Benign

0.43

PhyloP100

-2.1

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=98/2

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.12

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over