chr4-17909343-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001394446.1(LCORL):c.433C>T(p.Leu145Phe) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000704 in 1,420,194 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001394446.1 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LCORL | NM_001394446.1 | c.433C>T | p.Leu145Phe | missense_variant, splice_region_variant | 5/8 | ENST00000635767.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LCORL | ENST00000635767.2 | c.433C>T | p.Leu145Phe | missense_variant, splice_region_variant | 5/8 | 5 | NM_001394446.1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000443 AC: 1AN: 225610Hom.: 0 AF XY: 0.00000815 AC XY: 1AN XY: 122652
GnomAD4 exome AF: 0.00000704 AC: 10AN: 1420194Hom.: 0 Cov.: 27 AF XY: 0.00000709 AC XY: 5AN XY: 705374
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 15, 2021 | The c.433C>T (p.L145F) alteration is located in exon 5 (coding exon 5) of the LCORL gene. This alteration results from a C to T substitution at nucleotide position 433, causing the leucine (L) at amino acid position 145 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