NM_001013615.3:c.289C>T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001013615.3(LURAP1):c.289C>T(p.Arg97Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,461,804 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LURAP1 | ENST00000371980.4 | c.289C>T | p.Arg97Trp | missense_variant | Exon 2 of 2 | 1 | NM_001013615.3 | ENSP00000361048.3 | ||
POMGNT1 | ENST00000371992.1 | c.-135G>A | 5_prime_UTR_variant | Exon 1 of 23 | 2 | ENSP00000361060.1 | ||||
POMGNT1 | ENST00000693223.1 | n.514G>A | non_coding_transcript_exon_variant | Exon 1 of 20 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251200Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135768
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461804Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727200
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.289C>T (p.R97W) alteration is located in exon 2 (coding exon 2) of the LURAP1 gene. This alteration results from a C to T substitution at nucleotide position 289, causing the arginine (R) at amino acid position 97 to be replaced by a tryptophan (W). 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