Variant chr15-58432184-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000236.3(LIPC):c.88+64A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0249 in 1,220,094 control chromosomes in the GnomAD database, including 1,063 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.055 ( 453 hom., cov: 32)

Exomes 𝑓: 0.021 ( 610 hom. )

Consequence

LIPC
NM_000236.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.183

Variant links:

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 links:

ALDH1A2 (HGNC:15472): (aldehyde dehydrogenase 1 family member A2) This protein belongs to the aldehyde dehydrogenase family of proteins. The product of this gene is an enzyme that catalyzes the synthesis of retinoic acid (RA) from retinaldehyde. Retinoic acid, the active derivative of vitamin A (retinol), is a hormonal signaling molecule that functions in developing and adult tissues. The studies of a similar mouse gene suggest that this enzyme and the cytochrome CYP26A1, concurrently establish local embryonic retinoic acid levels which facilitate posterior organ development and prevent spina bifida. Four transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, May 2011]

ALDH1A2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

BP6

Variant 15-58432184-A-G is Benign according to our data. Variant chr15-58432184-A-G is described in ClinVar as [Benign]. Clinvar id is 1243737.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LIPC	NM_000236.3 linkuse as main transcript	c.88+64A>G		intron_variant		ENST00000299022.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LIPC	ENST00000299022.10 linkuse as main transcript	c.88+64A>G		intron_variant		1	NM_000236.3	P1

Frequencies

GnomAD3 genomes

AF:

0.0546

AC:

8312

AN:

152178

Hom.:

450

Cov.:

show subpopulations

Gnomad AFR

AF:

0.137

Gnomad AMI

AF:

0.00987

Gnomad AMR

AF:

0.0472

Gnomad ASJ

AF:

0.0274

Gnomad EAS

AF:

0.0638

Gnomad SAS

AF:

0.0553

Gnomad FIN

AF:

0.0298

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0112

Gnomad OTH

AF:

0.0501

GnomAD4 exome

AF:

0.0207

AC:

22078

AN:

1067798

Hom.:

610

Cov.:

AF XY:

0.0211

AC XY:

11620

AN XY:

549612

show subpopulations

Gnomad4 AFR exome

AF:

0.142

Gnomad4 AMR exome

AF:

0.0408

Gnomad4 ASJ exome

AF:

0.0301

Gnomad4 EAS exome

AF:

0.0591

Gnomad4 SAS exome

AF:

0.0438

Gnomad4 FIN exome

AF:

0.0248

Gnomad4 NFE exome

AF:

0.00964

Gnomad4 OTH exome

AF:

0.0301

GnomAD4 genome

AF:

0.0547

AC:

8324

AN:

152296

Hom.:

453

Cov.:

AF XY:

0.0556

AC XY:

4143

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.137

Gnomad4 AMR

AF:

0.0472

Gnomad4 ASJ

AF:

0.0274

Gnomad4 EAS

AF:

0.0638

Gnomad4 SAS

AF:

0.0551

Gnomad4 FIN

AF:

0.0298

Gnomad4 NFE

AF:

0.0112

Gnomad4 OTH

AF:

0.0496

Alfa

AF:

0.0201

Hom.:

145

Bravo

AF:

0.0591

Asia WGS

AF:

0.0570

AC:

201

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 18, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

5.9

DANN

Benign

0.77

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over