ENST00000414170.7:c.-40-2745A>G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000414170.7(LIPC):c.-40-2745A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 141,412 control chromosomes in the GnomAD database, including 998 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 0.11 ( 998 hom., cov: 29)
Consequence
LIPC
ENST00000414170.7 intron
ENST00000414170.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.934
Publications
5 publications found
Genes affected
LIPC (HGNC:6619): (lipase C, hepatic type) Enables phospholipase A1 activity and triglyceride lipase activity. Involved in several processes, including lipid homeostasis; plasma lipoprotein particle remodeling; and triglyceride catabolic process. Located in extracellular space. Implicated in several diseases, including Alzheimer's disease; coronary artery disease; familial combined hyperlipidemia; peripheral vascular disease; and type 2 diabetes mellitus. Biomarker of hyperinsulinism; obesity; and type 1 diabetes mellitus. [provided by Alliance of Genome Resources, Apr 2022]
ALDH1A2 (HGNC:15472): (aldehyde dehydrogenase 1 family member A2) This protein belongs to the aldehyde dehydrogenase family of proteins. The product of this gene is an enzyme that catalyzes the synthesis of retinoic acid (RA) from retinaldehyde. Retinoic acid, the active derivative of vitamin A (retinol), is a hormonal signaling molecule that functions in developing and adult tissues. The studies of a similar mouse gene suggest that this enzyme and the cytochrome CYP26A1, concurrently establish local embryonic retinoic acid levels which facilitate posterior organ development and prevent spina bifida. Four transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, May 2011]
ALDH1A2 Gene-Disease associations (from GenCC):
- diaphragmatic hernia 4, with cardiovascular defectsInheritance: AR Classification: STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
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=-0.98).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LIPC | ENST00000414170.7 | c.-40-2745A>G | intron_variant | Intron 1 of 9 | 1 | ENSP00000395569.3 | ||||
LIPC | ENST00000356113.10 | c.-365-1579A>G | intron_variant | Intron 1 of 10 | 2 | ENSP00000348425.6 | ||||
ALDH1A2 | ENST00000558239.5 | c.-306-9143T>C | intron_variant | Intron 1 of 3 | 4 | ENSP00000453292.1 |
Frequencies
GnomAD3 genomes AF: 0.107 AC: 15145AN: 141348Hom.: 1000 Cov.: 29 show subpopulations
GnomAD3 genomes
AF:
AC:
15145
AN:
141348
Hom.:
Cov.:
29
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.107 AC: 15134AN: 141412Hom.: 998 Cov.: 29 AF XY: 0.109 AC XY: 7462AN XY: 68220 show subpopulations
GnomAD4 genome
AF:
AC:
15134
AN:
141412
Hom.:
Cov.:
29
AF XY:
AC XY:
7462
AN XY:
68220
show subpopulations
African (AFR)
AF:
AC:
1060
AN:
37242
American (AMR)
AF:
AC:
1093
AN:
13020
Ashkenazi Jewish (ASJ)
AF:
AC:
460
AN:
3416
East Asian (EAS)
AF:
AC:
316
AN:
4624
South Asian (SAS)
AF:
AC:
702
AN:
4518
European-Finnish (FIN)
AF:
AC:
1647
AN:
8910
Middle Eastern (MID)
AF:
AC:
24
AN:
274
European-Non Finnish (NFE)
AF:
AC:
9547
AN:
66558
Other (OTH)
AF:
AC:
194
AN:
1954
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
639
1278
1918
2557
3196
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
176
352
528
704
880
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
347
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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