10-88665570-T-C

Position:

• chr10-88665570-T-C

Variant summary

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

The NM_004190.4(LIPF):​c.-12+1079T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 1,528,326 control chromosomes in the GnomAD database, including 56,114 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 0.27 (5760 hom., cov: 31)
  • Exomes 𝑓: 0.27 (50354 hom.)
• Consequence: LIPF NM_004190.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880

Genes affected

LIPF (HGNC:6622): (lipase F, gastric type) This gene encodes gastric lipase, an enzyme involved in the digestion of dietary triglycerides in the gastrointestinal tract, and responsible for 30% of fat digestion processes occurring in human. It is secreted by gastric chief cells in the fundic mucosa of the stomach, and it hydrolyzes the ester bonds of triglycerides under acidic pH conditions. The gene is a member of a conserved gene family of lipases that play distinct roles in neutral lipid metabolism. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2010]

LIPF (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LIPF	NM_004190.4	c.-12+1079T>C		intron_variant		ENST00000238983.9	NP_004181.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LIPF	ENST00000238983.9	c.-12+1079T>C		intron_variant		1	NM_004190.4	ENSP00000238983.5

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41416 AN: 151852 Hom.: 5746 Cov.: 31

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.299

GnomAD3 exomes AF: 0.293 AC: 39391 AN: 134440 Hom.: 5919 AF XY: 0.293 AC XY: 21437 AN XY: 73226

Gnomad AFR exome AF: 0.254

Gnomad AMR exome AF: 0.311

Gnomad ASJ exome AF: 0.344

Gnomad EAS exome AF: 0.368

Gnomad SAS exome AF: 0.307

Gnomad FIN exome AF: 0.255

Gnomad NFE exome AF: 0.264

Gnomad OTH exome AF: 0.299

GnomAD4 exome AF: 0.266 AC: 366752 AN: 1376356 Hom.: 50354 Cov.: 29 AF XY: 0.268 AC XY: 182334 AN XY: 679524

Gnomad4 AFR exome AF: 0.261

Gnomad4 AMR exome AF: 0.318

Gnomad4 ASJ exome AF: 0.342

Gnomad4 EAS exome AF: 0.393

Gnomad4 SAS exome AF: 0.302

Gnomad4 FIN exome AF: 0.258

Gnomad4 NFE exome AF: 0.255

Gnomad4 OTH exome AF: 0.288

GnomAD4 genome AF: 0.273 AC: 41465 AN: 151970 Hom.: 5760 Cov.: 31 AF XY: 0.274 AC XY: 20348 AN XY: 74278

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.300

Alfa AF: 0.251 Hom.: 2091

Bravo AF: 0.277

Asia WGS AF: 0.348 AC: 1211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
DANN	Benign	0.70

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: rs814624; hg19: chr10-90425327; COSMIC: COSV53286009;