10-88727381-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001080518.2(LIPK):c.223+469C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 184,084 control chromosomes in the GnomAD database, including 54,707 homozygotes. 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: 𝑓 0.78 ( 46973 hom., cov: 33)
Exomes 𝑓: 0.69 ( 7734 hom. )
Consequence
LIPK
NM_001080518.2 intron
NM_001080518.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0100
Genes affected
LIPK (HGNC:23444): (lipase family member K) Predicted to enable lipoprotein lipase activity. Predicted to be involved in cornification. Predicted to be located in extracellular region. Predicted to be active in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.777 AC: 118167AN: 152100Hom.: 46905 Cov.: 33
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GnomAD4 exome AF: 0.685 AC: 21840AN: 31866Hom.: 7734 AF XY: 0.695 AC XY: 11177AN XY: 16076
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GnomAD4 genome AF: 0.777 AC: 118295AN: 152218Hom.: 46973 Cov.: 33 AF XY: 0.781 AC XY: 58124AN XY: 74410
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ClinVar
Not reported inComputational scores
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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