chr10-88737768-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001080518.2(LIPK):c.803A>C(p.Gln268Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000384 in 1,613,810 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001080518.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIPK | NM_001080518.2 | c.803A>C | p.Gln268Pro | missense_variant | 7/10 | ENST00000404190.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIPK | ENST00000404190.3 | c.803A>C | p.Gln268Pro | missense_variant | 7/10 | 1 | NM_001080518.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000985 AC: 15AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000145 AC: 36AN: 248978Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135068
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461472Hom.: 0 Cov.: 31 AF XY: 0.0000220 AC XY: 16AN XY: 727006
GnomAD4 genome ? AF: 0.0000985 AC: 15AN: 152338Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74504
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 12, 2022 | The c.803A>C (p.Q268P) alteration is located in exon 6 (coding exon 6) of the LIPK gene. This alteration results from a A to C substitution at nucleotide position 803, causing the glutamine (Q) at amino acid position 268 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at