chr18-49594946-G-T

Position:

• chr18-49594946-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006033.4(LIPG):​c.*4424G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,098 control chromosomes in the GnomAD database, including 7,578 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 0.31 (7578 hom., cov: 33)
  • Exomes 𝑓: 0.10 (0 hom.)
• Consequence: LIPG NM_006033.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LIPG	NM_006033.4	c.*4424G>T		3_prime_UTR_variant	10/10	ENST00000261292.9	NP_006024.1
LIPG	NM_001308006.2	c.*4424G>T		3_prime_UTR_variant	9/9		NP_001294935.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LIPG	ENST00000261292.9	c.*4424G>T		3_prime_UTR_variant	10/10	1	NM_006033.4	ENSP00000261292.4

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47316 AN: 151970 Hom.: 7570 Cov.: 33

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.311

GnomAD4 exome AF: 0.100 AC: 1 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.100 AC XY: 1 AN XY: 10

Gnomad4 NFE exome AF: 0.100

GnomAD4 genome AF: 0.311 AC: 47369 AN: 152088 Hom.: 7578 Cov.: 33 AF XY: 0.319 AC XY: 23714 AN XY: 74340

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.311

Alfa AF: 0.309 Hom.: 6976

Bravo AF: 0.305

Asia WGS AF: 0.361 AC: 1259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.62
DANN	Benign	0.42

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

LitVar

Other links and lift over

dbSNP: rs17798991; hg19: chr18-47121316;