Genetic Variant LIPF:c.422+523T>C (chr10-88669279-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004190.4(LIPF):c.422+523T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 158,072 control chromosomes in the GnomAD database, including 3,100 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 0.19 ( 2982 hom., cov: 32)

Exomes 𝑓: 0.18 ( 118 hom. )

Consequence

LIPF
NM_004190.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.79

Publications

3 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004190.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LIPF	NM_004190.4	MANE Select	c.422+523T>C	intron	N/A	NP_004181.1	P07098-1
LIPF	NM_001198829.2		c.452+523T>C	intron	N/A	NP_001185758.1	P07098-3
LIPF	NM_001198830.2		c.353+523T>C	intron	N/A	NP_001185759.1	P07098-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LIPF	ENST00000238983.9	TSL:1 MANE Select	c.422+523T>C	intron	N/A	ENSP00000238983.5	P07098-1
LIPF	ENST00000355843.2	TSL:1	c.353+523T>C	intron	N/A	ENSP00000348101.3	P07098-4
LIPF	ENST00000609378.1	TSL:1	n.1006T>C	non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.190

AC:

28900

AN:

151988

Hom.:

2975

Cov.:

show subpopulations

Gnomad AFR

AF:

0.125

Gnomad AMI

AF:

0.113

Gnomad AMR

AF:

0.237

Gnomad ASJ

AF:

0.269

Gnomad EAS

AF:

0.307

Gnomad SAS

AF:

0.233

Gnomad FIN

AF:

0.138

Gnomad MID

AF:

0.222

Gnomad NFE

AF:

0.212

Gnomad OTH

AF:

0.210

GnomAD4 exome

AF:

0.181

AC:

1079

AN:

5966

Hom.:

118

Cov.:

AF XY:

0.176

AC XY:

549

AN XY:

3116

show subpopulations

African (AFR)

AF:

0.167

AC:

AN:

American (AMR)

AF:

0.164

AC:

245

AN:

1490

Ashkenazi Jewish (ASJ)

AF:

0.167

AC:

AN:

East Asian (EAS)

AF:

0.264

AC:

AN:

178

South Asian (SAS)

AF:

0.163

AC:

109

AN:

668

European-Finnish (FIN)

AF:

0.0818

AC:

AN:

110

Middle Eastern (MID)

AF:

0.250

AC:

AN:

European-Non Finnish (NFE)

AF:

0.189

AC:

618

AN:

3270

Other (OTH)

AF:

0.211

AC:

AN:

204

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

127

170

212

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.190

AC:

28930

AN:

152106

Hom.:

2982

Cov.:

AF XY:

0.190

AC XY:

14100

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.126

AC:

5210

AN:

41482

American (AMR)

AF:

0.237

AC:

3612

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.269

AC:

933

AN:

3470

East Asian (EAS)

AF:

0.308

AC:

1588

AN:

5164

South Asian (SAS)

AF:

0.234

AC:

1126

AN:

4812

European-Finnish (FIN)

AF:

0.138

AC:

1464

AN:

10602

Middle Eastern (MID)

AF:

0.221

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.212

AC:

14387

AN:

67996

Other (OTH)

AF:

0.209

AC:

442

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1173

2346

3518

4691

5864

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

316

632

948

1264

1580

<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:

0.201

Hom.:

1329

Bravo

AF:

0.192

Asia WGS

AF:

0.259

AC:

901

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.27

(source)

DANN

Benign

0.54

PhyloP100

-1.8

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over