10-89213641-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000235.4(LIPA):c.*1187C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0264 in 152,170 control chromosomes in the GnomAD database, including 176 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000235.4 3_prime_UTR
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LIPA | NM_000235.4 | c.*1187C>A | 3_prime_UTR_variant | Exon 10 of 10 | ENST00000336233.10 | NP_000226.2 | ||
LIPA | NM_001127605.3 | c.*1187C>A | 3_prime_UTR_variant | Exon 10 of 10 | NP_001121077.1 | |||
LIPA | NM_001288979.2 | c.*1187C>A | 3_prime_UTR_variant | Exon 8 of 8 | NP_001275908.1 | |||
LIPA | XM_024448023.2 | c.*1187C>A | 3_prime_UTR_variant | Exon 10 of 10 | XP_024303791.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LIPA | ENST00000336233 | c.*1187C>A | 3_prime_UTR_variant | Exon 10 of 10 | 1 | NM_000235.4 | ENSP00000337354.5 | |||
LIPA | ENST00000371837 | c.*1187C>A | 3_prime_UTR_variant | Exon 9 of 9 | 2 | ENSP00000360903.1 | ||||
LIPA | ENST00000456827 | c.*1187C>A | 3_prime_UTR_variant | Exon 8 of 8 | 3 | ENSP00000413019.2 |
Frequencies
GnomAD3 genomes AF: 0.0265 AC: 4023AN: 152052Hom.: 177 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 66Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 44
GnomAD4 genome AF: 0.0264 AC: 4024AN: 152170Hom.: 176 Cov.: 32 AF XY: 0.0251 AC XY: 1867AN XY: 74400
ClinVar
Submissions by phenotype
Wolman disease Benign:1
- -
Lysosomal acid lipase deficiency Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at