rs2097055
Positions:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_006033.4(LIPG):c.460-320T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 151,824 control chromosomes in the GnomAD database, including 23,640 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).
Frequency
Genomes: 𝑓 0.55 ( 23640 hom., cov: 31)
Consequence
LIPG
NM_006033.4 intron
NM_006033.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.222
Genes affected
LIPG (HGNC:6623): (lipase G, endothelial type) The protein encoded by this gene has substantial phospholipase activity and may be involved in lipoprotein metabolism and vascular biology. This protein is designated a member of the TG lipase family by its sequence and characteristic lid region which provides substrate specificity for enzymes of the TG lipase family. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BP6
?
Variant 18-49569117-T-C is Benign according to our data. Variant chr18-49569117-T-C is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIPG | NM_006033.4 | c.460-320T>C | intron_variant | ENST00000261292.9 | |||
LIPG | NM_001308006.2 | c.460-320T>C | intron_variant | ||||
LIPG | XM_047437944.1 | c.568-320T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIPG | ENST00000261292.9 | c.460-320T>C | intron_variant | 1 | NM_006033.4 | P1 | |||
LIPG | ENST00000580036.5 | c.460-320T>C | intron_variant | 1 | |||||
LIPG | ENST00000427224.6 | c.460-320T>C | intron_variant | 2 | |||||
LIPG | ENST00000577628.5 | c.568-320T>C | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.551 AC: 83517AN: 151706Hom.: 23621 Cov.: 31
GnomAD3 genomes
?
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.550 AC: 83563AN: 151824Hom.: 23640 Cov.: 31 AF XY: 0.543 AC XY: 40267AN XY: 74164
GnomAD4 genome
?
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31
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40267
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74164
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1614
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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