Genetic Variant LIPG:c.*482A>G (chr18-49591004-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.*482A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 252,156 control chromosomes in the GnomAD database, including 16,105 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 0.36 ( 10107 hom., cov: 32)

Exomes 𝑓: 0.33 ( 5998 hom. )

Consequence

LIPG
NM_006033.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.06

Publications

11 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:

Genome browser will be placed here

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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LIPG	NM_006033.4 link	c.*482A>G		3_prime_UTR_variant	Exon 10 of 10	ENST00000261292.9	NP_006024.1	Q9Y5X9-1A0A024R2B5
LIPG	NM_001308006.2 link	c.*482A>G		3_prime_UTR_variant	Exon 9 of 9		NP_001294935.1	Q9Y5X9B4DTR8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIPG	ENST00000261292.9 link	c.*482A>G		3_prime_UTR_variant	Exon 10 of 10	1	NM_006033.4	ENSP00000261292.4		Q9Y5X9-1
LIPG	ENST00000623277.1 link	n.1646A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes

AF:

0.358

AC:

54350

AN:

151854

Hom.:

10090

Cov.:

show subpopulations

Gnomad AFR

AF:

0.390

Gnomad AMI

AF:

0.206

Gnomad AMR

AF:

0.363

Gnomad ASJ

AF:

0.372

Gnomad EAS

AF:

0.634

Gnomad SAS

AF:

0.270

Gnomad FIN

AF:

0.452

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.311

Gnomad OTH

AF:

0.338

GnomAD4 exome

AF:

0.330

AC:

33017

AN:

100182

Hom.:

5998

Cov.:

AF XY:

0.326

AC XY:

16945

AN XY:

51914

show subpopulations

African (AFR)

AF:

0.373

AC:

1488

AN:

3986

American (AMR)

AF:

0.382

AC:

1916

AN:

5020

Ashkenazi Jewish (ASJ)

AF:

0.367

AC:

901

AN:

2452

East Asian (EAS)

AF:

0.638

AC:

3687

AN:

5778

South Asian (SAS)

AF:

0.255

AC:

3443

AN:

13478

European-Finnish (FIN)

AF:

0.393

AC:

1732

AN:

4412

Middle Eastern (MID)

AF:

0.225

AC:

AN:

396

European-Non Finnish (NFE)

AF:

0.304

AC:

18042

AN:

59300

Other (OTH)

AF:

0.321

AC:

1719

AN:

5360

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1004

2007

3011

4014

5018

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

238

476

714

952

1190

<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:

0.358

AC:

54417

AN:

151974

Hom.:

10107

Cov.:

AF XY:

0.365

AC XY:

27101

AN XY:

74254

show subpopulations

African (AFR)

AF:

0.390

AC:

16162

AN:

41428

American (AMR)

AF:

0.363

AC:

5549

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.372

AC:

1292

AN:

3472

East Asian (EAS)

AF:

0.634

AC:

3260

AN:

5140

South Asian (SAS)

AF:

0.271

AC:

1306

AN:

4820

European-Finnish (FIN)

AF:

0.452

AC:

4777

AN:

10566

Middle Eastern (MID)

AF:

0.214

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.311

AC:

21102

AN:

67952

Other (OTH)

AF:

0.341

AC:

719

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1775

3551

5326

7102

8877

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

534

1068

1602

2136

2670

<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:

0.342

Hom.:

5025

Bravo

AF:

0.356

Asia WGS

AF:

0.477

AC:

1661

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.24

(source)

DANN

Benign

0.32

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over