chr10-88669866-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004190.4(LIPF):c.452C>T(p.Pro151Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000411 in 1,460,706 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004190.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LIPF | ENST00000238983.9 | c.452C>T | p.Pro151Leu | missense_variant | Exon 5 of 10 | 1 | NM_004190.4 | ENSP00000238983.5 | ||
LIPF | ENST00000355843.2 | c.383C>T | p.Pro128Leu | missense_variant | Exon 6 of 11 | 1 | ENSP00000348101.3 | |||
LIPF | ENST00000394375.7 | c.482C>T | p.Pro161Leu | missense_variant | Exon 6 of 11 | 2 | ENSP00000377900.3 | |||
LIPF | ENST00000608620.5 | c.353C>T | p.Pro118Leu | missense_variant | Exon 5 of 10 | 2 | ENSP00000477140.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251038Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135658
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1460706Hom.: 0 Cov.: 29 AF XY: 0.00000413 AC XY: 3AN XY: 726680
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.482C>T (p.P161L) alteration is located in exon 6 (coding exon 5) of the LIPF gene. This alteration results from a C to T substitution at nucleotide position 482, causing the proline (P) at amino acid position 161 to be replaced by a leucine (L). 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