10-89214220-G-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_000235.4(LIPA):​c.*608C>A variant causes a 3 prime UTR 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: 33)

Consequence

LIPA
NM_000235.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.195
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LIPANM_000235.4 linkc.*608C>A 3_prime_UTR_variant Exon 10 of 10 ENST00000336233.10 NP_000226.2 P38571-1
LIPANM_001127605.3 linkc.*608C>A 3_prime_UTR_variant Exon 10 of 10 NP_001121077.1 P38571-1
LIPANM_001288979.2 linkc.*608C>A 3_prime_UTR_variant Exon 8 of 8 NP_001275908.1 P38571A0A0A0MT32
LIPAXM_024448023.2 linkc.*608C>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
LIPAENST00000336233 linkc.*608C>A 3_prime_UTR_variant Exon 10 of 10 1 NM_000235.4 ENSP00000337354.5 P38571-1
LIPAENST00000371837 linkc.*608C>A 3_prime_UTR_variant Exon 9 of 9 2 ENSP00000360903.1 P38571-2
LIPAENST00000456827 linkc.*608C>A 3_prime_UTR_variant Exon 8 of 8 3 ENSP00000413019.2 A0A0A0MT32

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
0
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.57
DANN
Benign
0.72

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9664201; hg19: chr10-90973977; API