chr15-58561164-C-T

Position:

• chr15-58561164-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000236.3(LIPC):​c.1169+183C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.925 in 152,238 control chromosomes in the GnomAD database, including 65,667 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.92 (65667 hom., cov: 33)
• Consequence: LIPC NM_000236.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.772

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP6: Variant 15-58561164-C-T is Benign according to our data. Variant chr15-58561164-C-T is described in ClinVar as [Benign]. Clinvar id is 1248145.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-58561164-C-T is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.979 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LIPC	NM_000236.3	c.1169+183C>T		intron_variant		ENST00000299022.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LIPC	ENST00000299022.10	c.1169+183C>T		intron_variant		1	NM_000236.3	P1

Frequencies

GnomAD3 genomes AF: 0.925 AC: 140757 AN: 152120 Hom.: 65652 Cov.: 33

Gnomad AFR AF: 0.788

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.972

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.985

Gnomad FIN AF: 0.947

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.985

Gnomad OTH AF: 0.941

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

GnomAD4 genome AF: 0.925 AC: 140809 AN: 152238 Hom.: 65667 Cov.: 33 AF XY: 0.926 AC XY: 68931 AN XY: 74448

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.973

Gnomad4 ASJ AF: 0.988

Gnomad4 EAS AF: 0.936

Gnomad4 SAS AF: 0.985

Gnomad4 FIN AF: 0.947

Gnomad4 NFE AF: 0.985

Gnomad4 OTH AF: 0.942

Alfa AF: 0.949 Hom.: 8561

Bravo AF: 0.921

Asia WGS AF: 0.945 AC: 3287 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 30, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.0
DANN	Benign	0.19

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: rs1869129; hg19: chr15-58853363;