20-63737994-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017806.4(LIME1):c.202C>T(p.Leu68Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000828 in 1,570,570 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017806.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LIME1 | NM_017806.4 | c.202C>T | p.Leu68Phe | missense_variant | Exon 4 of 6 | ENST00000309546.8 | NP_060276.2 | |
LIME1 | NM_001305654.2 | c.181-14C>T | intron_variant | Intron 3 of 5 | NP_001292583.1 | |||
LIME1 | NM_001305655.2 | c.181-14C>T | intron_variant | Intron 3 of 5 | NP_001292584.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LIME1 | ENST00000309546.8 | c.202C>T | p.Leu68Phe | missense_variant | Exon 4 of 6 | 1 | NM_017806.4 | ENSP00000309521.3 | ||
ENSG00000273154 | ENST00000632538.1 | c.520-14C>T | intron_variant | Intron 4 of 5 | 3 | ENSP00000488802.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152146Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000569 AC: 1AN: 175894Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 96628
GnomAD4 exome AF: 0.00000776 AC: 11AN: 1418424Hom.: 0 Cov.: 50 AF XY: 0.00000996 AC XY: 7AN XY: 702686
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152146Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.202C>T (p.L68F) alteration is located in exon 4 (coding exon 3) of the LIME1 gene. This alteration results from a C to T substitution at nucleotide position 202, causing the leucine (L) at amino acid position 68 to be replaced by a phenylalanine (F). 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