chr18-49594946-G-T

Variant names:

• chr18-49594946-G-T
• rs17798991
• NM_006033.4:c.*4424G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.404 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPG	NM_006033.4	MANE Select	c.*4424G>T		3_prime_UTR	Exon 10 of 10	NP_006024.1	Q9Y5X9-1
	LIPG	NM_001308006.2		c.*4424G>T		3_prime_UTR	Exon 9 of 9	NP_001294935.1	B4DTR8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPG	ENST00000261292.9	TSL:1 MANE Select	c.*4424G>T		3_prime_UTR	Exon 10 of 10	ENSP00000261292.4	Q9Y5X9-1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.100 AC: 1 AN: 10

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.260 AC: 10787 AN: 41486

American (AMR) AF: 0.347 AC: 5304 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1275 AN: 3468

East Asian (EAS) AF: 0.419 AC: 2161 AN: 5160

South Asian (SAS) AF: 0.251 AC: 1209 AN: 4824

European-Finnish (FIN) AF: 0.449 AC: 4746 AN: 10572

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 20983 AN: 67984

Other (OTH) AF: 0.311 AC: 656 AN: 2110

Alfa AF: 0.310 Hom.: 18045

Bravo AF: 0.305

Asia WGS AF: 0.361 AC: 1259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.62
DANN	Benign	0.42
PhyloP100		-0.37

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: rs17798991; hg19: chr18-47121316;