rs61729804

Variant names:

• chr18-49565437-C-A
• NM_006033.4:c.218C>A

Your query was ambiguous. Multiple possible variants found:

• chr18-49565437-C-A
• chr18-49565437-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_006033.4(LIPG):​c.218C>A​(p.Pro73His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,894 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict 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: 6.8e-7 (0 hom.)
• Consequence: LIPG NM_006033.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900

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 Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.09285277).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LIPG	NM_006033.4	c.218C>A	p.Pro73His	missense_variant	Exon 2 of 10	ENST00000261292.9	NP_006024.1
LIPG	NM_001308006.2	c.218C>A	p.Pro73His	missense_variant	Exon 2 of 9		NP_001294935.1
LIPG	XM_047437944.1	c.326C>A	p.Pro109His	missense_variant	Exon 2 of 5		XP_047293900.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIPG	ENST00000261292.9	c.218C>A	p.Pro73His	missense_variant	Exon 2 of 10	1	NM_006033.4	ENSP00000261292.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461894 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 727248

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.069
BayesDel_addAF	Benign	-0.024	T
BayesDel_noAF	Benign	-0.27
CADD	Benign	0.77
DANN	Benign	0.70
DEOGEN2	Benign	0.27	T;T;T;.
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.13	N
LIST_S2	Benign	0.39	T;T;T;T
M_CAP	Benign	0.048	D
MetaRNN	Benign	0.093	T;T;T;T
MetaSVM	Benign	-0.67	T
MutationAssessor	Benign	0.40	.;N;.;N
PrimateAI	Benign	0.26	T
PROVEAN	Benign	-0.58	.;N;N;.
REVEL	Benign	0.26
Sift	Benign	0.061	.;T;T;.
Sift4G	Benign	0.17	T;T;T;T
Polyphen		0.0, 0.0010	.;B;B;B
Vest4		0.13
MutPred		0.45		.;Gain of catalytic residue at E75 (P = 0.0654);Gain of catalytic residue at E75 (P = 0.0654);Gain of catalytic residue at E75 (P = 0.0654);
MVP		0.85
MPC		0.41
ClinPred		0.067	T
GERP RS		-1.5
Varity_R		0.18
gMVP		0.29

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr18-47091807; COSMIC: COSV54298356;