chr18-49560748-G-A

Variant names:

• chr18-49560748-G-A
• rs3829632
• ENST00000577628.5:c.-938G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000577628.5(LIPG):​c.-938G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,266 control chromosomes in the GnomAD database, including 52,661 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 0.82 (52643 hom., cov: 32)
  • Exomes 𝑓: 0.83 (18 hom.)
• Consequence: LIPG ENST00000577628.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 5 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000577628.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPG	ENST00000577628.5	TSL:2	c.-938G>A		5_prime_UTR	Exon 1 of 6	ENSP00000463835.1

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125359 AN: 152096 Hom.: 52591 Cov.: 32

Gnomad AFR AF: 0.956

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.844

GnomAD4 exome AF: 0.827 AC: 43 AN: 52 Hom.: 18 Cov.: 0 AF XY: 0.868 AC XY: 33 AN XY: 38

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 1.00 AC: 4 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.800 AC: 32 AN: 40

Other (OTH) AF: 0.750 AC: 3 AN: 4

GnomAD4 genome AF: 0.824 AC: 125461 AN: 152214 Hom.: 52643 Cov.: 32 AF XY: 0.818 AC XY: 60881 AN XY: 74416

African (AFR) AF: 0.957 AC: 39753 AN: 41556

American (AMR) AF: 0.666 AC: 10171 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.877 AC: 3042 AN: 3470

East Asian (EAS) AF: 0.547 AC: 2832 AN: 5176

South Asian (SAS) AF: 0.830 AC: 3999 AN: 4818

European-Finnish (FIN) AF: 0.730 AC: 7720 AN: 10582

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.810 AC: 55121 AN: 68020

Other (OTH) AF: 0.846 AC: 1781 AN: 2106

Alfa AF: 0.831 Hom.: 7790

Bravo AF: 0.821

Asia WGS AF: 0.723 AC: 2513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.0
DANN	Benign	0.74
PhyloP100		0.30
PromoterAI		0.064	Neutral
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3829632; hg19: chr18-47087118;