11-24983267-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001009909.4(LUZP2):c.739C>T(p.Leu247Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,459,940 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L247P) has been classified as Uncertain significance.
Frequency
Consequence
NM_001009909.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LUZP2 | ENST00000336930.11 | c.739C>T | p.Leu247Phe | missense_variant | Exon 9 of 12 | 1 | NM_001009909.4 | ENSP00000336817.6 | ||
LUZP2 | ENST00000533227.5 | c.481C>T | p.Leu161Phe | missense_variant | Exon 9 of 12 | 1 | ENSP00000432952.1 | |||
LUZP2 | ENST00000620308.1 | c.481C>T | p.Leu161Phe | missense_variant | Exon 8 of 11 | 5 | ENSP00000480441.1 | |||
LUZP2 | ENST00000529015.5 | c.*85C>T | downstream_gene_variant | 4 | ENSP00000437032.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250212Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135248
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1459940Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726276
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at