chr18-49560628-A-C

Variant names:

• chr18-49560628-A-C
• rs4245232
• ENST00000577628.5:c.-1058A>C

Variant summary

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

The ENST00000577628.5(LIPG):​c.-1058A>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,260 control chromosomes in the GnomAD database, including 52,628 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 (52618 hom., cov: 33)
  • Exomes 𝑓: 0.91 (10 hom.)
• Consequence: LIPG ENST00000577628.5 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.800
• Publications: 4 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=-0.94).
• 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPG	ENST00000577628.5	TSL:2	c.-1058A>C		upstream_gene	N/A	ENSP00000463835.1

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125320 AN: 152120 Hom.: 52566 Cov.: 33

Gnomad AFR AF: 0.956

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.933

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.842

GnomAD4 exome AF: 0.909 AC: 20 AN: 22 Hom.: 10 AF XY: 0.833 AC XY: 10 AN XY: 12

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) AF: 1.00 AC: 8 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.857 AC: 12 AN: 14

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.824 AC: 125422 AN: 152238 Hom.: 52618 Cov.: 33 AF XY: 0.818 AC XY: 60842 AN XY: 74414

African (AFR) AF: 0.957 AC: 39764 AN: 41572

American (AMR) AF: 0.664 AC: 10155 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.877 AC: 3040 AN: 3468

East Asian (EAS) AF: 0.548 AC: 2838 AN: 5178

South Asian (SAS) AF: 0.830 AC: 4003 AN: 4824

European-Finnish (FIN) AF: 0.729 AC: 7708 AN: 10576

Middle Eastern (MID) AF: 0.938 AC: 274 AN: 292

European-Non Finnish (NFE) AF: 0.810 AC: 55092 AN: 68018

Other (OTH) AF: 0.844 AC: 1782 AN: 2112

Alfa AF: 0.811 Hom.: 183309

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	-0.94
CADD	Benign	8.6
DANN	Benign	0.35
PhyloP100		0.80
PromoterAI		0.061	Neutral
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs4245232; hg19: chr18-47086998;