chr10-89215892-G-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000235.4(LIPA):c.966+46C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
LIPA
NM_000235.4 intron
NM_000235.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.270
Publications
0 publications found
Genes affected
LIPA (HGNC:6617): (lipase A, lysosomal acid type) This gene encodes lipase A, the lysosomal acid lipase (also known as cholesterol ester hydrolase). This enzyme functions in the lysosome to catalyze the hydrolysis of cholesteryl esters and triglycerides. Mutations in this gene can result in Wolman disease and cholesteryl ester storage disease. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2014]
LIPA Gene-Disease associations (from GenCC):
- lysosomal acid lipase deficiencyInheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Genomics England PanelApp, ClinGen, Myriad Women’s Health, Labcorp Genetics (formerly Invitae)
- cholesteryl ester storage diseaseInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- Wolman diseaseInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LIPA | ENST00000336233.10 | c.966+46C>A | intron_variant | Intron 9 of 9 | 1 | NM_000235.4 | ENSP00000337354.5 | |||
LIPA | ENST00000371837.5 | c.798+46C>A | intron_variant | Intron 8 of 8 | 2 | ENSP00000360903.1 | ||||
LIPA | ENST00000456827.5 | c.618+46C>A | intron_variant | Intron 7 of 7 | 3 | ENSP00000413019.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1098338Hom.: 0 Cov.: 15 AF XY: 0.00 AC XY: 0AN XY: 563200
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1098338
Hom.:
Cov.:
15
AF XY:
AC XY:
0
AN XY:
563200
African (AFR)
AF:
AC:
0
AN:
26348
American (AMR)
AF:
AC:
0
AN:
44288
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
23912
East Asian (EAS)
AF:
AC:
0
AN:
38100
South Asian (SAS)
AF:
AC:
0
AN:
78944
European-Finnish (FIN)
AF:
AC:
0
AN:
53274
Middle Eastern (MID)
AF:
AC:
0
AN:
5026
European-Non Finnish (NFE)
AF:
AC:
0
AN:
780050
Other (OTH)
AF:
AC:
0
AN:
48396
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
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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