chr10-88730991-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001080518.2(LIPK):c.232C>T(p.Pro78Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000108 in 1,578,668 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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 1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152168Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000984 AC: 2AN: 203246Hom.: 0 AF XY: 0.00000917 AC XY: 1AN XY: 109060
GnomAD4 exome AF: 0.0000105 AC: 15AN: 1426500Hom.: 0 Cov.: 32 AF XY: 0.0000127 AC XY: 9AN XY: 706540
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152168Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.232C>T (p.P78S) alteration is located in exon 3 (coding exon 3) of the LIPK gene. This alteration results from a C to T substitution at nucleotide position 232, causing the proline (P) at amino acid position 78 to be replaced by a serine (S). 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