Genetic Variant LIPG:c.793+142A>G (chr18-49575732-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006033.4(LIPG):c.793+142A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.815 in 741,070 control chromosomes in the GnomAD database, including 250,539 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 0.84 ( 54977 hom., cov: 32)

Exomes 𝑓: 0.81 ( 195562 hom. )

Consequence

LIPG
NM_006033.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.13

Publications

9 publications found

Variant links:

Genes affected

LIPG (HGNC:6623): (lipase G, endothelial type) The protein encoded by this gene has substantial phospholipase activity and may be involved in lipoprotein metabolism and vascular biology. This protein is designated a member of the TG lipase family by its sequence and characteristic lid region which provides substrate specificity for enzymes of the TG lipase family. [provided by RefSeq, Jul 2008]

LIPG links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006033.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPG	NM_006033.4	MANE Select	c.793+142A>G		intron	N/A	NP_006024.1
	LIPG	NM_001308006.2		c.572-5683A>G		intron	N/A	NP_001294935.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
LIPG	ENST00000261292.9	TSL:1 MANE Select	c.793+142A>G	intron	N/A	ENSP00000261292.4
LIPG	ENST00000580036.5	TSL:1	c.793+142A>G	intron	N/A	ENSP00000462420.1
LIPG	ENST00000427224.6	TSL:2	c.572-5683A>G	intron	N/A	ENSP00000387978.2

Frequencies

GnomAD3 genomes

AF:

0.843

AC:

128188

AN:

152036

Hom.:

54922

Cov.:

show subpopulations

Gnomad AFR

AF:

0.964

Gnomad AMI

AF:

0.847

Gnomad AMR

AF:

0.677

Gnomad ASJ

AF:

0.883

Gnomad EAS

AF:

0.559

Gnomad SAS

AF:

0.850

Gnomad FIN

AF:

0.756

Gnomad MID

AF:

0.934

Gnomad NFE

AF:

0.839

Gnomad OTH

AF:

0.856

GnomAD4 exome

AF:

0.808

AC:

475651

AN:

588916

Hom.:

195562

AF XY:

0.814

AC XY:

257015

AN XY:

315646

show subpopulations

African (AFR)

AF:

0.963

AC:

15537

AN:

16132

American (AMR)

AF:

0.595

AC:

19872

AN:

33404

Ashkenazi Jewish (ASJ)

AF:

0.877

AC:

17207

AN:

19618

East Asian (EAS)

AF:

0.510

AC:

16400

AN:

32188

South Asian (SAS)

AF:

0.863

AC:

52698

AN:

61038

European-Finnish (FIN)

AF:

0.754

AC:

25159

AN:

33376

Middle Eastern (MID)

AF:

0.918

AC:

2320

AN:

2528

European-Non Finnish (NFE)

AF:

0.837

AC:

300400

AN:

359078

Other (OTH)

AF:

0.826

AC:

26058

AN:

31554

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.519

Heterozygous variant carriers

4596

9192

13788

18384

22980

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2122

4244

6366

8488

10610

<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:

0.843

AC:

128295

AN:

152154

Hom.:

54977

Cov.:

AF XY:

0.836

AC XY:

62198

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.964

AC:

40052

AN:

41552

American (AMR)

AF:

0.676

AC:

10334

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.883

AC:

3067

AN:

3472

East Asian (EAS)

AF:

0.559

AC:

2885

AN:

5158

South Asian (SAS)

AF:

0.849

AC:

4103

AN:

4832

European-Finnish (FIN)

AF:

0.756

AC:

7958

AN:

10530

Middle Eastern (MID)

AF:

0.939

AC:

276

AN:

294

European-Non Finnish (NFE)

AF:

0.839

AC:

57038

AN:

68010

Other (OTH)

AF:

0.858

AC:

1813

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

967

1934

2901

3868

4835

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

888

1776

2664

3552

4440

<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:

0.844

Hom.:

31995

Bravo

AF:

0.838

Asia WGS

AF:

0.738

AC:

2565

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.31

(source)

DANN

Benign

0.46

PhyloP100

-1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over