NM_006033.4:c.*482A>G

Variant names:

• chr18-49591004-A-G
• rs3744841
• NM_006033.4:c.*482A>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.*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
• Publications: 11 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 = 0.616 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPG	NM_006033.4	MANE Select	c.*482A>G		3_prime_UTR	Exon 10 of 10	NP_006024.1
	LIPG	NM_001308006.2		c.*482A>G		3_prime_UTR	Exon 9 of 9	NP_001294935.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPG	ENST00000261292.9	TSL:1 MANE Select	c.*482A>G		3_prime_UTR	Exon 10 of 10	ENSP00000261292.4
	LIPG	ENST00000623277.1	TSL:6	n.1646A>G		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.373 AC: 1488 AN: 3986

American (AMR) AF: 0.382 AC: 1916 AN: 5020

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 901 AN: 2452

East Asian (EAS) AF: 0.638 AC: 3687 AN: 5778

South Asian (SAS) AF: 0.255 AC: 3443 AN: 13478

European-Finnish (FIN) AF: 0.393 AC: 1732 AN: 4412

Middle Eastern (MID) AF: 0.225 AC: 89 AN: 396

European-Non Finnish (NFE) AF: 0.304 AC: 18042 AN: 59300

Other (OTH) AF: 0.321 AC: 1719 AN: 5360

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

African (AFR) AF: 0.390 AC: 16162 AN: 41428

American (AMR) AF: 0.363 AC: 5549 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1292 AN: 3472

East Asian (EAS) AF: 0.634 AC: 3260 AN: 5140

South Asian (SAS) AF: 0.271 AC: 1306 AN: 4820

European-Finnish (FIN) AF: 0.452 AC: 4777 AN: 10566

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.311 AC: 21102 AN: 67952

Other (OTH) AF: 0.341 AC: 719 AN: 2106

Alfa AF: 0.342 Hom.: 5025

Bravo AF: 0.356

Asia WGS AF: 0.477 AC: 1661 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	0.24
DANN	Benign	0.32
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: rs3744841; hg19: chr18-47117374;