rs1229406

Variant names:

• chr10-88670852-G-C
• rs1229406
• NM_004190.4:c.532+906G>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.532+906G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,134 control chromosomes in the GnomAD database, including 1,841 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 0.14 (1841 hom., cov: 32)
• Consequence: LIPF NM_004190.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.725
• Publications: 0 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LIPF	NM_004190.4	c.532+906G>C		intron_variant	Intron 5 of 9	ENST00000238983.9	NP_004181.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIPF	ENST00000238983.9	c.532+906G>C		intron_variant	Intron 5 of 9	1	NM_004190.4	ENSP00000238983.5
LIPF	ENST00000355843.2	c.463+906G>C		intron_variant	Intron 6 of 10	1		ENSP00000348101.3
LIPF	ENST00000394375.7	c.562+906G>C		intron_variant	Intron 6 of 10	2		ENSP00000377900.3
LIPF	ENST00000608620.5	c.433+906G>C		intron_variant	Intron 5 of 9	2		ENSP00000477140.1

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21230 AN: 152016 Hom.: 1839 Cov.: 32

Gnomad AFR AF: 0.0414

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.140 AC: 21227 AN: 152134 Hom.: 1841 Cov.: 32 AF XY: 0.141 AC XY: 10494 AN XY: 74370

African (AFR) AF: 0.0413 AC: 1715 AN: 41544

American (AMR) AF: 0.187 AC: 2848 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 644 AN: 3468

East Asian (EAS) AF: 0.307 AC: 1582 AN: 5156

South Asian (SAS) AF: 0.218 AC: 1052 AN: 4830

European-Finnish (FIN) AF: 0.126 AC: 1336 AN: 10578

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11629 AN: 67974

Other (OTH) AF: 0.149 AC: 314 AN: 2110

Alfa AF: 0.145 Hom.: 210

Bravo AF: 0.137

Asia WGS AF: 0.247 AC: 860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.7
DANN	Benign	0.73
PhyloP100		-0.72
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1229406; hg19: chr10-90430609;