10-89225233-G-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_000235.4(LIPA):c.539-5C>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000347 in 1,613,898 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000235.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIPA | NM_000235.4 | c.539-5C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000336233.10 | |||
LIPA | NM_001127605.3 | c.539-5C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
LIPA | NM_001288979.2 | c.191-5C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
LIPA | XM_024448023.2 | c.539-5C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIPA | ENST00000336233.10 | c.539-5C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000235.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 152038Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251068Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135730
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461742Hom.: 0 Cov.: 34 AF XY: 0.0000151 AC XY: 11AN XY: 727188
GnomAD4 genome AF: 0.000204 AC: 31AN: 152156Hom.: 1 Cov.: 32 AF XY: 0.000229 AC XY: 17AN XY: 74382
ClinVar
Submissions by phenotype
Lysosomal acid lipase deficiency Uncertain:1Benign:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Jul 28, 2020 | - - |
Likely benign, no assertion criteria provided | clinical testing | Elsea Laboratory, Baylor College of Medicine | Apr 01, 2020 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Oct 06, 2017 | - - |
Wolman disease Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 09, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at