rs1444780892

Variant names:

• chr18-49562344-C-G
• NM_006033.4:c.36C>G

Your query was ambiguous. Multiple possible variants found:

• chr18-49562344-C-G
• chr18-49562344-C-T

Variant summary

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

The NM_006033.4(LIPG):​c.36C>G​(p.Ser12Arg) 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 1,461,114 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: LIPG NM_006033.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225

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 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LIPG	NM_006033.4	c.36C>G	p.Ser12Arg	missense_variant	Exon 1 of 10	ENST00000261292.9	NP_006024.1
LIPG	NM_001308006.2	c.36C>G	p.Ser12Arg	missense_variant	Exon 1 of 9		NP_001294935.1
LIPG	XM_047437944.1	c.205+454C>G		intron_variant	Intron 1 of 4		XP_047293900.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIPG	ENST00000261292.9	c.36C>G	p.Ser12Arg	missense_variant	Exon 1 of 10	1	NM_006033.4	ENSP00000261292.4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461114 Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0 AN XY: 726820

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 8.99e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.38
BayesDel_addAF	Uncertain	0.044	T
BayesDel_noAF	Benign	-0.17
CADD	Benign	14
DANN	Uncertain	0.99
DEOGEN2	Benign	0.091	T;T;.
Eigen	Benign	-0.64
Eigen_PC	Benign	-0.67
FATHMM_MKL	Benign	0.10	N
LIST_S2	Benign	0.70	T;T;T
M_CAP	Uncertain	0.10	D
MetaRNN	Uncertain	0.65	D;D;D
MetaSVM	Benign	-0.57	T
MutationAssessor	Benign	1.8	L;.;L
PrimateAI	Benign	0.42	T
PROVEAN	Benign	-1.0	N;N;.
REVEL	Uncertain	0.35
Sift	Benign	0.059	T;D;.
Sift4G	Benign	0.39	T;T;T
Polyphen		0.66	P;P;P
Vest4		0.20
MutPred		0.74		Loss of catalytic residue at L8 (P = 0.1222);Loss of catalytic residue at L8 (P = 0.1222);Loss of catalytic residue at L8 (P = 0.1222);
MVP		0.94
MPC		0.49
ClinPred		0.54	D
GERP RS		2.1
Varity_R		0.12
gMVP		0.54

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: chr18-47088714;