rs36041167

chr15-58431398-G-A

Variant summary

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

The ENST00000414170.7(LIPC):c.-40-595G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0445 in 518,692 control chromosomes in the GnomAD database, including 706 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 0.038 (157 hom., cov: 32)
  • Exomes 𝑓: 0.047 (549 hom.)
• Consequence: LIPC ENST00000414170.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300

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]

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LIPC	ENST00000414170.7	c.-40-595G>A		intron_variant		1
LIPC	ENST00000356113.10	c.-41+247G>A		intron_variant		2		P1
ALDH1A2	ENST00000558239.5	c.-306-11293C>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0383 AC: 5832 AN: 152130 Hom.: 157 Cov.: 32

Gnomad AFR AF: 0.00992

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0388

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0497

Gnomad FIN AF: 0.0326

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0574

Gnomad OTH AF: 0.0502

GnomAD4 exome AF: 0.0471 AC: 17271 AN: 366444 Hom.: 549 AF XY: 0.0497 AC XY: 10442 AN XY: 210112

Gnomad4 AFR exome AF: 0.00943

Gnomad4 AMR exome AF: 0.0198

Gnomad4 ASJ exome AF: 0.0603

Gnomad4 EAS exome AF: 0.000228

Gnomad4 SAS exome AF: 0.0534

Gnomad4 FIN exome AF: 0.0341

Gnomad4 NFE exome AF: 0.0549

Gnomad4 OTH exome AF: 0.0490

GnomAD4 genome AF: 0.0383 AC: 5832 AN: 152248 Hom.: 157 Cov.: 32 AF XY: 0.0366 AC XY: 2721 AN XY: 74438

Gnomad4 AFR AF: 0.00989

Gnomad4 AMR AF: 0.0387

Gnomad4 ASJ AF: 0.0533

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0500

Gnomad4 FIN AF: 0.0326

Gnomad4 NFE AF: 0.0574

Gnomad4 OTH AF: 0.0497

Alfa AF: 0.0542 Hom.: 139

Bravo AF: 0.0372

Asia WGS AF: 0.0260 AC: 91 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	0.76
Dann	Benign	0.33

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: rs36041167; hg19: chr15-58723597;