Genetic Variant LIPG:c.-1124C>T (chr18-49560562-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000577628.5(LIPG):c.-1124C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,224 control chromosomes in the GnomAD database, including 52,656 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 0.82 ( 52646 hom., cov: 32)

Exomes 𝑓: 0.92 ( 10 hom. )

Consequence

LIPG
ENST00000577628.5 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.732

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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIPG	ENST00000577628.5 link	c.-1124C>T		upstream_gene_variant		2		ENSP00000463835.1		J3QQQ0

Frequencies

GnomAD3 genomes

AF:

0.824

AC:

125357

AN:

152082

Hom.:

52594

Cov.:

show subpopulations

Gnomad AFR

AF:

0.957

Gnomad AMI

AF:

0.840

Gnomad AMR

AF:

0.666

Gnomad ASJ

AF:

0.876

Gnomad EAS

AF:

0.547

Gnomad SAS

AF:

0.831

Gnomad FIN

AF:

0.730

Gnomad MID

AF:

0.933

Gnomad NFE

AF:

0.811

Gnomad OTH

AF:

0.841

GnomAD4 exome

AF:

0.917

AC:

AN:

Hom.:

AF XY:

0.938

AC XY:

AN XY:

show subpopulations

Gnomad4 SAS exome

AF:

1.00

Gnomad4 FIN exome

AF:

0.750

Gnomad4 NFE exome

AF:

1.00

Gnomad4 OTH exome

AF:

1.00

GnomAD4 genome

AF:

0.824

AC:

125459

AN:

152200

Hom.:

52646

Cov.:

AF XY:

0.818

AC XY:

60858

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.957

Gnomad4 AMR

AF:

0.665

Gnomad4 ASJ

AF:

0.876

Gnomad4 EAS

AF:

0.547

Gnomad4 SAS

AF:

0.830

Gnomad4 FIN

AF:

0.730

Gnomad4 NFE

AF:

0.811

Gnomad4 OTH

AF:

0.844

Alfa

AF:

0.823

Hom.:

58294

Bravo

AF:

0.821

Asia WGS

AF:

0.723

AC:

2514

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

0.19

DANN

Benign

0.46

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over