18-49591004-A-T

Variant names:

• chr18-49591004-A-T
• rs3744841
• NM_006033.4:c.*482A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_006033.4(LIPG):​c.*482A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LIPG	NM_006033.4	c.*482A>T		3_prime_UTR_variant	Exon 10 of 10	ENST00000261292.9	NP_006024.1
LIPG	NM_001308006.2	c.*482A>T		3_prime_UTR_variant	Exon 9 of 9		NP_001294935.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIPG	ENST00000261292.9	c.*482A>T		3_prime_UTR_variant	Exon 10 of 10	1	NM_006033.4	ENSP00000261292.4
LIPG	ENST00000623277.1	n.1646A>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 100420 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 52016

African (AFR) AF: 0.00 AC: 0 AN: 3998

American (AMR) AF: 0.00 AC: 0 AN: 5022

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2458

East Asian (EAS) AF: 0.00 AC: 0 AN: 5784

South Asian (SAS) AF: 0.00 AC: 0 AN: 13512

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4422

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 396

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 59458

Other (OTH) AF: 0.00 AC: 0 AN: 5370

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.21
DANN	Benign	0.47
PhyloP100		-1.1

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;