rs3819166

Variant names:

• chr18-49575732-A-G
• rs3819166
• NM_006033.4:c.793+142A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• 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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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 rank	MANE	Protein	UniProt
LIPG	NM_006033.4	c.793+142A>G		intron_variant	Intron 5 of 9	ENST00000261292.9	NP_006024.1
LIPG	NM_001308006.2	c.572-5683A>G		intron_variant	Intron 4 of 8		NP_001294935.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIPG	ENST00000261292.9	c.793+142A>G		intron_variant	Intron 5 of 9	1	NM_006033.4	ENSP00000261292.4
LIPG	ENST00000580036.5	c.793+142A>G		intron_variant	Intron 5 of 5	1		ENSP00000462420.1
LIPG	ENST00000427224.6	c.572-5683A>G		intron_variant	Intron 4 of 8	2		ENSP00000387978.2
LIPG	ENST00000577628.5	c.901+142A>G		intron_variant	Intron 5 of 5	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

African (AFR) AF: 0.963 AC: 15537 AN: 16132

American (AMR) AF: 0.595 AC: 19872 AN: 33404

Ashkenazi Jewish (ASJ) AF: 0.877 AC: 17207 AN: 19618

East Asian (EAS) AF: 0.510 AC: 16400 AN: 32188

South Asian (SAS) AF: 0.863 AC: 52698 AN: 61038

European-Finnish (FIN) AF: 0.754 AC: 25159 AN: 33376

Middle Eastern (MID) AF: 0.918 AC: 2320 AN: 2528

European-Non Finnish (NFE) AF: 0.837 AC: 300400 AN: 359078

Other (OTH) AF: 0.826 AC: 26058 AN: 31554

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

African (AFR) AF: 0.964 AC: 40052 AN: 41552

American (AMR) AF: 0.676 AC: 10334 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.883 AC: 3067 AN: 3472

East Asian (EAS) AF: 0.559 AC: 2885 AN: 5158

South Asian (SAS) AF: 0.849 AC: 4103 AN: 4832

European-Finnish (FIN) AF: 0.756 AC: 7958 AN: 10530

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 57038 AN: 68010

Other (OTH) AF: 0.858 AC: 1813 AN: 2112

Alfa AF: 0.844 Hom.: 31995

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
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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