dbSNP rs3813082: LIPG:c.-13A>C (chr18-49561673-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000577628.5(LIPG):c.-13A>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00769 in 1,239,728 control chromosomes in the GnomAD database, including 513 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 0.017 ( 110 hom., cov: 33)

Exomes 𝑓: 0.0063 ( 403 hom. )

Consequence

LIPG
ENST00000577628.5 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.579

Publications

12 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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LIPG	XM_047437944.1 link	c.-13A>C		5_prime_UTR_variant	Exon 1 of 5		XP_047293900.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIPG	ENST00000577628.5 link	c.-13A>C		5_prime_UTR_variant	Exon 1 of 6	2		ENSP00000463835.1		J3QQQ0
LIPG	ENST00000583083.1 link	c.-144+213A>C		intron_variant	Intron 1 of 2	3		ENSP00000463077.1		J3KTN7

Frequencies

GnomAD3 genomes

AF:

0.0175

AC:

2656

AN:

152194

Hom.:

109

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0298

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00536

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.192

Gnomad SAS

AF:

0.0431

Gnomad FIN

AF:

0.00226

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00112

Gnomad OTH

AF:

0.0177

GnomAD2 exomes

AF:

0.0189

AC:

AN:

2540

AF XY:

0.0156

show subpopulations

Gnomad AFR exome

AF:

0.0600

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.110

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00632

AC:

6871

AN:

1087416

Hom.:

403

Cov.:

AF XY:

0.00602

AC XY:

3090

AN XY:

513664

show subpopulations

African (AFR)

AF:

0.0311

AC:

715

AN:

22996

American (AMR)

AF:

0.00233

AC:

AN:

10302

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14434

East Asian (EAS)

AF:

0.143

AC:

3835

AN:

26848

South Asian (SAS)

AF:

0.0398

AC:

804

AN:

20186

European-Finnish (FIN)

AF:

0.00372

AC:

AN:

21210

Middle Eastern (MID)

AF:

0.00445

AC:

AN:

2924

European-Non Finnish (NFE)

AF:

0.000515

AC:

476

AN:

924540

Other (OTH)

AF:

0.0210

AC:

925

AN:

43976

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

355

710

1065

1420

1775

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

126

252

378

504

630

<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:

0.0175

AC:

2663

AN:

152312

Hom.:

110

Cov.:

AF XY:

0.0189

AC XY:

1404

AN XY:

74472

show subpopulations

African (AFR)

AF:

0.0300

AC:

1246

AN:

41570

American (AMR)

AF:

0.00536

AC:

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3468

East Asian (EAS)

AF:

0.191

AC:

987

AN:

5168

South Asian (SAS)

AF:

0.0427

AC:

206

AN:

4824

European-Finnish (FIN)

AF:

0.00226

AC:

AN:

10626

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00112

AC:

AN:

68024

Other (OTH)

AF:

0.0194

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

134

268

401

535

669

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

114

152

190

<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:

0.00418

Hom.:

Bravo

AF:

0.0188

Asia WGS

AF:

0.105

AC:

365

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

(source)

DANN

Benign

0.54

PhyloP100

0.58

PromoterAI

0.0059

Neutral

(source)

Mutation Taster

=299/1

polymorphism (auto)

(source)

Splicing

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