rs3829632

Positions:

• chr18-49560748-G-A
• chr18-49560748-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000577628.5(LIPG):​c.-938G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,266 control chromosomes in the GnomAD database, including 52,661 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 (52643 hom., cov: 32)
  • Exomes 𝑓: 0.83 (18 hom.)
• Consequence: LIPG ENST00000577628.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LIPG	ENST00000577628.5	c.-938G>A		5_prime_UTR_variant	1/6	2		ENSP00000463835

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125359 AN: 152096 Hom.: 52591 Cov.: 32

Gnomad AFR AF: 0.956

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.844

GnomAD4 exome AF: 0.827 AC: 43 AN: 52 Hom.: 18 Cov.: 0 AF XY: 0.868 AC XY: 33 AN XY: 38

Gnomad4 AFR exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.800

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.824 AC: 125461 AN: 152214 Hom.: 52643 Cov.: 32 AF XY: 0.818 AC XY: 60881 AN XY: 74416

Gnomad4 AFR AF: 0.957

Gnomad4 AMR AF: 0.666

Gnomad4 ASJ AF: 0.877

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.830

Gnomad4 FIN AF: 0.730

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.846

Alfa AF: 0.831 Hom.: 7790

Bravo AF: 0.821

Asia WGS AF: 0.723 AC: 2513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.0
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3829632; hg19: chr18-47087118;