rs3744841

chr18-49591004-A-Gchr18-49591004-A-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

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=-0.9).
• 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/exons	MANE	UniProt
LIPG	NM_006033.4	c.*482A>G		3_prime_UTR_variant	10/10	ENST00000261292.9
LIPG	NM_001308006.2	c.*482A>G		3_prime_UTR_variant	9/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LIPG	ENST00000261292.9	c.*482A>G		3_prime_UTR_variant	10/10	1	NM_006033.4	P1
LIPG	ENST00000623277.1	n.1646A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54350 AN: 151854 Hom.: 10090 Cov.: 32

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.: 0 AF XY: 0.326 AC XY: 16945 AN XY: 51914

Gnomad4 AFR exome AF: 0.373

Gnomad4 AMR exome AF: 0.382

Gnomad4 ASJ exome AF: 0.367

Gnomad4 EAS exome AF: 0.638

Gnomad4 SAS exome AF: 0.255

Gnomad4 FIN exome AF: 0.393

Gnomad4 NFE exome AF: 0.304

Gnomad4 OTH exome AF: 0.321

GnomAD4 genome AF: 0.358 AC: 54417 AN: 151974 Hom.: 10107 Cov.: 32 AF XY: 0.365 AC XY: 27101 AN XY: 74254

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.634

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.341

Alfa AF: 0.333 Hom.: 2060

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
Dann	Benign	0.32

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

LitVar

Other links and lift over

dbSNP: rs3744841; hg19: chr18-47117374;