rs9664201
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_000235.4(LIPA):c.*608C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00411 in 151,458 control chromosomes in the GnomAD database, including 7 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
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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.*608C>T | 3_prime_UTR_variant | Exon 10 of 10 | ENST00000336233.10 | NP_000226.2 | ||
LIPA | NM_001127605.3 | c.*608C>T | 3_prime_UTR_variant | Exon 10 of 10 | NP_001121077.1 | |||
LIPA | NM_001288979.2 | c.*608C>T | 3_prime_UTR_variant | Exon 8 of 8 | NP_001275908.1 | |||
LIPA | XM_024448023.2 | c.*608C>T | 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.*608C>T | 3_prime_UTR_variant | Exon 10 of 10 | 1 | NM_000235.4 | ENSP00000337354.5 | |||
LIPA | ENST00000371837 | c.*608C>T | 3_prime_UTR_variant | Exon 9 of 9 | 2 | ENSP00000360903.1 | ||||
LIPA | ENST00000456827 | c.*608C>T | 3_prime_UTR_variant | Exon 8 of 8 | 3 | ENSP00000413019.2 |
Frequencies
GnomAD3 genomes AF: 0.00408 AC: 618AN: 151346Hom.: 7 Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 216Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 130
GnomAD4 genome AF: 0.00411 AC: 623AN: 151458Hom.: 7 Cov.: 33 AF XY: 0.00427 AC XY: 316AN XY: 74062
ClinVar
Submissions by phenotype
Lysosomal acid lipase deficiency Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at