rs3819166

Positions:

• chr18-49575732-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The NM_006033.4(LIPG):​c.793+142A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.815 in 741,070 control chromosomes in the GnomAD database, including 250,539 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.84 (54977 hom., cov: 32)
  • Exomes 𝑓: 0.81 (195562 hom.)
• Consequence: LIPG NM_006033.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 18-49575732-A-G is Benign according to our data. Variant chr18-49575732-A-G is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LIPG	NM_006033.4	c.793+142A>G		intron_variant		ENST00000261292.9	NP_006024.1
LIPG	NM_001308006.2	c.572-5683A>G		intron_variant			NP_001294935.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LIPG	ENST00000261292.9	c.793+142A>G		intron_variant		1	NM_006033.4	ENSP00000261292.4
LIPG	ENST00000580036.5	c.793+142A>G		intron_variant		1		ENSP00000462420.1
LIPG	ENST00000427224.6	c.572-5683A>G		intron_variant		2		ENSP00000387978.2
LIPG	ENST00000577628.5	c.901+142A>G		intron_variant		2		ENSP00000463835.1

Frequencies

GnomAD3 genomes AF: 0.843 AC: 128188 AN: 152036 Hom.: 54922 Cov.: 32

Gnomad AFR AF: 0.964

Gnomad AMI AF: 0.847

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.883

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.856

GnomAD4 exome AF: 0.808 AC: 475651 AN: 588916 Hom.: 195562 AF XY: 0.814 AC XY: 257015 AN XY: 315646

Gnomad4 AFR exome AF: 0.963

Gnomad4 AMR exome AF: 0.595

Gnomad4 ASJ exome AF: 0.877

Gnomad4 EAS exome AF: 0.510

Gnomad4 SAS exome AF: 0.863

Gnomad4 FIN exome AF: 0.754

Gnomad4 NFE exome AF: 0.837

Gnomad4 OTH exome AF: 0.826

GnomAD4 genome AF: 0.843 AC: 128295 AN: 152154 Hom.: 54977 Cov.: 32 AF XY: 0.836 AC XY: 62198 AN XY: 74370

Gnomad4 AFR AF: 0.964

Gnomad4 AMR AF: 0.676

Gnomad4 ASJ AF: 0.883

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.849

Gnomad4 FIN AF: 0.756

Gnomad4 NFE AF: 0.839

Gnomad4 OTH AF: 0.858

Alfa AF: 0.843 Hom.: 28872

Bravo AF: 0.838

Asia WGS AF: 0.738 AC: 2565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.31
DANN	Benign	0.46

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: rs3819166; hg19: chr18-47102102; COSMIC: COSV54299516;