chr15-58487442-C-A

Position:

• chr15-58487442-C-A

Variant summary

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

The NM_000236.3(LIPC):​c.89-50891C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0882 in 152,262 control chromosomes in the GnomAD database, including 734 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 0.088 (734 hom., cov: 33)
• Consequence: LIPC NM_000236.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658

Genes affected

LIPC (HGNC:6619): (lipase C, hepatic type) Enables phospholipase A1 activity and triglyceride lipase activity. Involved in several processes, including lipid homeostasis; plasma lipoprotein particle remodeling; and triglyceride catabolic process. Located in extracellular space. Implicated in several diseases, including Alzheimer's disease; coronary artery disease; familial combined hyperlipidemia; peripheral vascular disease; and type 2 diabetes mellitus. Biomarker of hyperinsulinism; obesity; and type 1 diabetes mellitus. [provided by Alliance of Genome Resources, Apr 2022]

LIPC (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LIPC	NM_000236.3	c.89-50891C>A		intron_variant		ENST00000299022.10	NP_000227.2
LIPC-AS1	NR_120338.1	n.208+7331G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LIPC	ENST00000299022.10	c.89-50891C>A		intron_variant		1	NM_000236.3	ENSP00000299022.5

Frequencies

GnomAD3 genomes AF: 0.0884 AC: 13443 AN: 152144 Hom.: 734 Cov.: 33

Gnomad AFR AF: 0.0238

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.0885

Gnomad ASJ AF: 0.0617

Gnomad EAS AF: 0.0849

Gnomad SAS AF: 0.0548

Gnomad FIN AF: 0.0961

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.0750

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0882 AC: 13435 AN: 152262 Hom.: 734 Cov.: 33 AF XY: 0.0853 AC XY: 6352 AN XY: 74462

Gnomad4 AFR AF: 0.0237

Gnomad4 AMR AF: 0.0885

Gnomad4 ASJ AF: 0.0617

Gnomad4 EAS AF: 0.0847

Gnomad4 SAS AF: 0.0545

Gnomad4 FIN AF: 0.0961

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.0742

Alfa AF: 0.116 Hom.: 1469

Bravo AF: 0.0855

Asia WGS AF: 0.0760 AC: 263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.4
DANN	Benign	0.84

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: rs12593880; hg19: chr15-58779641;