rs3813082

Positions:

• chr18-49561673-A-C
• chr18-49561673-A-G

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.579

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=-0.87).
• 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/exons	MANE	Protein	UniProt
LIPG	XM_047437944.1	c.-13A>C		5_prime_UTR_variant	1/5		XP_047293900.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LIPG	ENST00000577628.5	c.-13A>C		5_prime_UTR_variant	1/6	2		ENSP00000463835
LIPG	ENST00000583083.1	c.-144+213A>C		intron_variant		3		ENSP00000463077

Frequencies

GnomAD3 genomes AF: 0.0175 AC: 2656 AN: 152194 Hom.: 109 Cov.: 33

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

GnomAD3 exomes AF: 0.0189 AC: 48 AN: 2540 Hom.: 3 AF XY: 0.0156 AC XY: 22 AN XY: 1408

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 SAS exome AF: 0.0200

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.: 30 AF XY: 0.00602 AC XY: 3090 AN XY: 513664

Gnomad4 AFR exome AF: 0.0311

Gnomad4 AMR exome AF: 0.00233

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.143

Gnomad4 SAS exome AF: 0.0398

Gnomad4 FIN exome AF: 0.00372

Gnomad4 NFE exome AF: 0.000515

Gnomad4 OTH exome AF: 0.0210

GnomAD4 genome AF: 0.0175 AC: 2663 AN: 152312 Hom.: 110 Cov.: 33 AF XY: 0.0189 AC XY: 1404 AN XY: 74472

Gnomad4 AFR AF: 0.0300

Gnomad4 AMR AF: 0.00536

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.0427

Gnomad4 FIN AF: 0.00226

Gnomad4 NFE AF: 0.00112

Gnomad4 OTH AF: 0.0194

Alfa AF: 0.00354 Hom.: 0

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	10
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3813082; hg19: chr18-47088043;