NM_006033.4:c.794-633C>G

Variant names:

• chr18-49580782-C-G
• rs12970066
• NM_006033.4:c.794-633C>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.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
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006033.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPG	NM_006033.4	MANE Select	c.794-633C>G		intron	N/A	NP_006024.1	Q9Y5X9-1
	LIPG	NM_001308006.2		c.572-633C>G		intron	N/A	NP_001294935.1	B4DTR8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPG	ENST00000261292.9	TSL:1 MANE Select	c.794-633C>G		intron	N/A	ENSP00000261292.4	Q9Y5X9-1
	LIPG	ENST00000580036.5	TSL:1	c.794-633C>G		intron	N/A	ENSP00000462420.1	Q9Y5X9-2
	LIPG	ENST00000959465.1		c.794-642C>G		intron	N/A	ENSP00000629524.1

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

African (AFR) AF: 0.195 AC: 8086 AN: 41504

American (AMR) AF: 0.218 AC: 3337 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 944 AN: 3472

East Asian (EAS) AF: 0.321 AC: 1662 AN: 5172

South Asian (SAS) AF: 0.311 AC: 1502 AN: 4826

European-Finnish (FIN) AF: 0.268 AC: 2837 AN: 10574

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19417 AN: 67996

Other (OTH) AF: 0.287 AC: 607 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.56
PhyloP100		0.073
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: rs12970066; hg19: chr18-47107152;