Variant chr15-58432172-C-T 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+52C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 1,315,820 control chromosomes in the GnomAD database, including 13,239 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 1074 hom., cov: 32)

Exomes 𝑓: 0.14 ( 12165 hom. )

Consequence

LIPC
NM_000236.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.107

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=-0.61).

BP6

Variant 15-58432172-C-T is Benign according to our data. Variant chr15-58432172-C-T is described in ClinVar as [Benign]. Clinvar id is 1244570.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr15-58432172-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.144 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+52C>T		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+52C>T		intron_variant		1	NM_000236.3	P1

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15794

AN:

152104

Hom.:

1075

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0262

Gnomad AMI

AF:

0.101

Gnomad AMR

AF:

0.0776

Gnomad ASJ

AF:

0.142

Gnomad EAS

AF:

0.0573

Gnomad SAS

AF:

0.148

Gnomad FIN

AF:

0.165

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.146

Gnomad OTH

AF:

0.0936

GnomAD3 exomes

AF:

0.122

AC:

30468

AN:

249972

Hom.:

2169

AF XY:

0.129

AC XY:

17435

AN XY:

135196

show subpopulations

Gnomad AFR exome

AF:

0.0212

Gnomad AMR exome

AF:

0.0601

Gnomad ASJ exome

AF:

0.132

Gnomad EAS exome

AF:

0.0567

Gnomad SAS exome

AF:

0.152

Gnomad FIN exome

AF:

0.173

Gnomad NFE exome

AF:

0.147

Gnomad OTH exome

AF:

0.123

GnomAD4 exome

AF:

0.140

AC:

163205

AN:

1163598

Hom.:

12165

Cov.:

AF XY:

0.142

AC XY:

84048

AN XY:

593366

show subpopulations

Gnomad4 AFR exome

AF:

0.0228

Gnomad4 AMR exome

AF:

0.0650

Gnomad4 ASJ exome

AF:

0.131

Gnomad4 EAS exome

AF:

0.0446

Gnomad4 SAS exome

AF:

0.152

Gnomad4 FIN exome

AF:

0.167

Gnomad4 NFE exome

AF:

0.151

Gnomad4 OTH exome

AF:

0.127

GnomAD4 genome

AF:

0.104

AC:

15783

AN:

152222

Hom.:

1074

Cov.:

AF XY:

0.105

AC XY:

7807

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.0261

Gnomad4 AMR

AF:

0.0774

Gnomad4 ASJ

AF:

0.142

Gnomad4 EAS

AF:

0.0575

Gnomad4 SAS

AF:

0.148

Gnomad4 FIN

AF:

0.165

Gnomad4 NFE

AF:

0.146

Gnomad4 OTH

AF:

0.0921

Alfa

AF:

0.134

Hom.:

777

Bravo

AF:

0.0938

Asia WGS

AF:

0.100

AC:

347

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	clinical testing	GeneDx	Sep 21, 2018	This variant is associated with the following publications: (PMID: 14551916) -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

6.2

DANN

Benign

0.85

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