Genetic Variant LIPF:p.Gln322Gln (chr10-88678450-A-G) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.54

Publications

16 publications found

Variant links:

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 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LIPF	NM_004190.4 link	c.966A>G	p.Gln322Gln	synonymous_variant	Exon 10 of 10	ENST00000238983.9	NP_004181.1	P07098-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIPF	ENST00000238983.9 link	c.966A>G	p.Gln322Gln	synonymous_variant	Exon 10 of 10	1	NM_004190.4	ENSP00000238983.5		P07098-1

Frequencies

GnomAD3 genomes

AF:

0.198

AC:

30034

AN:

151854

Hom.:

3121

Cov.:

show subpopulations

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

GnomAD2 exomes

AF:

0.225

AC:

56586

AN:

251356

AF XY:

0.225

show subpopulations

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 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.:

AF XY:

0.210

AC XY:

152087

AN XY:

725652

show subpopulations

African (AFR)

AF:

0.137

AC:

4592

AN:

33446

American (AMR)

AF:

0.258

AC:

11534

AN:

44716

Ashkenazi Jewish (ASJ)

AF:

0.223

AC:

5824

AN:

26106

East Asian (EAS)

AF:

0.356

AC:

14103

AN:

39666

South Asian (SAS)

AF:

0.229

AC:

19692

AN:

86174

European-Finnish (FIN)

AF:

0.228

AC:

12161

AN:

53416

Middle Eastern (MID)

AF:

0.205

AC:

1179

AN:

5762

European-Non Finnish (NFE)

AF:

0.200

AC:

222113

AN:

1108878

Other (OTH)

AF:

0.216

AC:

13012

AN:

60282

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

11141

22281

33422

44562

55703

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7862

15724

23586

31448

39310

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.198

AC:

30046

AN:

151970

Hom.:

3128

Cov.:

AF XY:

0.200

AC XY:

14869

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.143

AC:

5937

AN:

41432

American (AMR)

AF:

0.249

AC:

3798

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.225

AC:

782

AN:

3472

East Asian (EAS)

AF:

0.341

AC:

1765

AN:

5170

South Asian (SAS)

AF:

0.241

AC:

1158

AN:

4814

European-Finnish (FIN)

AF:

0.214

AC:

2257

AN:

10562

Middle Eastern (MID)

AF:

0.207

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.202

AC:

13700

AN:

67952

Other (OTH)

AF:

0.204

AC:

431

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1223

2446

3668

4891

6114

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

332

664

996

1328

1660

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.202

Hom.:

10984

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

(source)

DANN

Benign

0.32

PhyloP100

-2.5

Mutation Taster

=89/11

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over