dbSNP rs3744841: 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

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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