10-88669279-T-C

Position:

• chr10-88669279-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.422+523T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 158,072 control chromosomes in the GnomAD database, including 3,100 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 0.19 (2982 hom., cov: 32)
  • Exomes 𝑓: 0.18 (118 hom.)
• Consequence: LIPF NM_004190.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

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 = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LIPF	NM_004190.4	c.422+523T>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.422+523T>C		intron_variant		1	NM_004190.4	ENSP00000238983.5

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28900 AN: 151988 Hom.: 2975 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.210

GnomAD4 exome AF: 0.181 AC: 1079 AN: 5966 Hom.: 118 Cov.: 0 AF XY: 0.176 AC XY: 549 AN XY: 3116

Gnomad4 AFR exome AF: 0.167

Gnomad4 AMR exome AF: 0.164

Gnomad4 ASJ exome AF: 0.167

Gnomad4 EAS exome AF: 0.264

Gnomad4 SAS exome AF: 0.163

Gnomad4 FIN exome AF: 0.0818

Gnomad4 NFE exome AF: 0.189

Gnomad4 OTH exome AF: 0.211

GnomAD4 genome AF: 0.190 AC: 28930 AN: 152106 Hom.: 2982 Cov.: 32 AF XY: 0.190 AC XY: 14100 AN XY: 74356

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.209

Alfa AF: 0.198 Hom.: 821

Bravo AF: 0.192

Asia WGS AF: 0.259 AC: 901 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	0.27
DANN	Benign	0.54

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: rs814626; hg19: chr10-90429036;