1-46203559-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001013615.3(LURAP1):c.133C>T(p.Leu45Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000319 in 1,566,666 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_001013615.3 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 |
---|---|---|---|---|---|---|---|---|---|---|
LURAP1 | ENST00000371980.4 | c.133C>T | p.Leu45Phe | missense_variant | Exon 1 of 2 | 1 | NM_001013615.3 | ENSP00000361048.3 | ||
POMGNT1 | ENST00000371992.1 | c.-50-5688G>A | intron_variant | Intron 1 of 22 | 2 | ENSP00000361060.1 | ||||
POMGNT1 | ENST00000693223.1 | n.599-5688G>A | intron_variant | Intron 1 of 19 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152116Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000500 AC: 1AN: 199810Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 108466
GnomAD4 exome AF: 0.00000141 AC: 2AN: 1414432Hom.: 0 Cov.: 30 AF XY: 0.00000142 AC XY: 1AN XY: 701968
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152234Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74434
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.133C>T (p.L45F) alteration is located in exon 1 (coding exon 1) of the LURAP1 gene. This alteration results from a C to T substitution at nucleotide position 133, causing the leucine (L) at amino acid position 45 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