chr3-185517333-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_139248.3(LIPH):c.887-171T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0955 in 152,186 control chromosomes in the GnomAD database, including 1,274 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.095 ( 1274 hom., cov: 32)
Consequence
LIPH
NM_139248.3 intron
NM_139248.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.24
Genes affected
LIPH (HGNC:18483): (lipase H) This gene encodes a membrane-bound member of the mammalian triglyceride lipase family. It catalyzes the production of 2-acyl lysophosphatidic acid (LPA), which is a lipid mediator with diverse biological properties that include platelet aggregation, smooth muscle contraction, and stimulation of cell proliferation and motility. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant 3-185517333-A-G is Benign according to our data. Variant chr3-185517333-A-G is described in ClinVar as [Benign]. Clinvar id is 1234223.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIPH | NM_139248.3 | c.887-171T>C | intron_variant | ENST00000296252.9 | |||
LIPH | XM_006713529.5 | c.797-171T>C | intron_variant | ||||
LIPH | XM_011512530.4 | c.758-171T>C | intron_variant | ||||
LIPH | XM_017005852.3 | c.785-171T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIPH | ENST00000296252.9 | c.887-171T>C | intron_variant | 1 | NM_139248.3 | P1 | |||
LIPH | ENST00000424591.6 | c.785-171T>C | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0954 AC: 14503AN: 152066Hom.: 1271 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0955 AC: 14529AN: 152186Hom.: 1274 Cov.: 32 AF XY: 0.0916 AC XY: 6815AN XY: 74404
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 20, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at