chr10-88677510-G-A

Position:

• chr10-88677510-G-A

Variant summary

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

The ENST00000238983.9(LIPF):​c.961-935G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 152,004 control chromosomes in the GnomAD database, including 22,543 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 0.53 (22543 hom., cov: 32)
• Consequence: LIPF ENST00000238983.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LIPF	NM_004190.4	c.961-935G>A		intron_variant		ENST00000238983.9	NP_004181.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LIPF	ENST00000238983.9	c.961-935G>A		intron_variant		1	NM_004190.4	ENSP00000238983	P1

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79745 AN: 151884 Hom.: 22497 Cov.: 32

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.508

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.525 AC: 79843 AN: 152004 Hom.: 22543 Cov.: 32 AF XY: 0.527 AC XY: 39130 AN XY: 74286

Gnomad4 AFR AF: 0.740

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.497

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.509

Alfa AF: 0.459 Hom.: 3742

Bravo AF: 0.541

Asia WGS AF: 0.574 AC: 1992 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.1
DANN	Benign	0.29

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs7913071; hg19: chr10-90437267;