rs1228187

Positions:

• chr10-88678450-A-G
• chr10-88678450-A-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_004190.4(LIPF):​c.966A>G​(p.Gln322Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 1,610,416 control chromosomes in the GnomAD database, including 35,934 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 0.20 (3128 hom., cov: 31)
  • Exomes 𝑓: 0.21 (32806 hom.)
• Consequence: LIPF NM_004190.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP7: Synonymous conserved (PhyloP=-2.54 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LIPF	NM_004190.4	c.966A>G	p.Gln322Gln	synonymous_variant	10/10	ENST00000238983.9	NP_004181.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LIPF	ENST00000238983.9	c.966A>G	p.Gln322Gln	synonymous_variant	10/10	1	NM_004190.4	ENSP00000238983.5

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30034 AN: 151854 Hom.: 3121 Cov.: 31

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.202

GnomAD3 exomes AF: 0.225 AC: 56586 AN: 251356 Hom.: 6592 AF XY: 0.225 AC XY: 30579 AN XY: 135842

Gnomad AFR exome AF: 0.142

Gnomad AMR exome AF: 0.254

Gnomad ASJ exome AF: 0.225

Gnomad EAS exome AF: 0.334

Gnomad SAS exome AF: 0.234

Gnomad FIN exome AF: 0.226

Gnomad NFE exome AF: 0.209

Gnomad OTH exome AF: 0.212

GnomAD4 exome AF: 0.209 AC: 304210 AN: 1458446 Hom.: 32806 Cov.: 31 AF XY: 0.210 AC XY: 152087 AN XY: 725652

Gnomad4 AFR exome AF: 0.137

Gnomad4 AMR exome AF: 0.258

Gnomad4 ASJ exome AF: 0.223

Gnomad4 EAS exome AF: 0.356

Gnomad4 SAS exome AF: 0.229

Gnomad4 FIN exome AF: 0.228

Gnomad4 NFE exome AF: 0.200

Gnomad4 OTH exome AF: 0.216

GnomAD4 genome AF: 0.198 AC: 30046 AN: 151970 Hom.: 3128 Cov.: 31 AF XY: 0.200 AC XY: 14869 AN XY: 74312

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.204

Alfa AF: 0.204 Hom.: 7065

Bravo AF: 0.198

Asia WGS AF: 0.296 AC: 1029 AN: 3478

EpiCase AF: 0.201

EpiControl AF: 0.208

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.047
DANN	Benign	0.32

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1228187; hg19: chr10-90438207; COSMIC: COSV53282603;