18-49580782-C-G

Position:

• chr18-49580782-C-G

Variant summary

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

The NM_006033.4(LIPG):​c.794-633C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,142 control chromosomes in the GnomAD database, including 5,082 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 0.25 (5082 hom., cov: 32)
• Consequence: LIPG NM_006033.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730

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 = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LIPG	NM_006033.4	c.794-633C>G		intron_variant		ENST00000261292.9	NP_006024.1
LIPG	NM_001308006.2	c.572-633C>G		intron_variant			NP_001294935.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LIPG	ENST00000261292.9	c.794-633C>G		intron_variant		1	NM_006033.4	ENSP00000261292.4
LIPG	ENST00000580036.5	c.794-633C>G		intron_variant		1		ENSP00000462420.1
LIPG	ENST00000427224.6	c.572-633C>G		intron_variant		2		ENSP00000387978.2
LIPG	ENST00000577628.5	c.902-633C>G		intron_variant		2		ENSP00000463835.1

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38780 AN: 152024 Hom.: 5089 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.289

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.255 AC: 38773 AN: 152142 Hom.: 5082 Cov.: 32 AF XY: 0.255 AC XY: 18993 AN XY: 74350

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.287

Alfa AF: 0.131 Hom.: 248

Bravo AF: 0.248

Asia WGS AF: 0.267 AC: 928 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	2.0
DANN	Benign	0.56

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: rs12970066; hg19: chr18-47107152;