rs3858282

Variant names:

• chr10-88674654-T-C
• rs3858282
• NM_004190.4:c.816+920T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004190.4(LIPF):​c.816+920T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 152,034 control chromosomes in the GnomAD database, including 12,138 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 0.39 (12138 hom., cov: 32)
• Consequence: LIPF NM_004190.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.958
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LIPF	NM_004190.4	c.816+920T>C		intron_variant	Intron 7 of 9	ENST00000238983.9	NP_004181.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIPF	ENST00000238983.9	c.816+920T>C		intron_variant	Intron 7 of 9	1	NM_004190.4	ENSP00000238983.5
LIPF	ENST00000355843.2	c.747+920T>C		intron_variant	Intron 8 of 10	1		ENSP00000348101.3
LIPF	ENST00000394375.7	c.846+920T>C		intron_variant	Intron 8 of 10	2		ENSP00000377900.3
LIPF	ENST00000608620.5	c.717+920T>C		intron_variant	Intron 7 of 9	2		ENSP00000477140.1

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59812 AN: 151916 Hom.: 12118 Cov.: 32

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.394 AC: 59876 AN: 152034 Hom.: 12138 Cov.: 32 AF XY: 0.398 AC XY: 29550 AN XY: 74314

African (AFR) AF: 0.486 AC: 20162 AN: 41454

American (AMR) AF: 0.394 AC: 6017 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1305 AN: 3470

East Asian (EAS) AF: 0.502 AC: 2594 AN: 5170

South Asian (SAS) AF: 0.453 AC: 2185 AN: 4826

European-Finnish (FIN) AF: 0.380 AC: 4012 AN: 10564

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22357 AN: 67964

Other (OTH) AF: 0.382 AC: 803 AN: 2102

Alfa AF: 0.350 Hom.: 40603

Bravo AF: 0.399

Asia WGS AF: 0.464 AC: 1610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.1
DANN	Benign	0.63
PhyloP100		0.96
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3858282; hg19: chr10-90434411;