1-46219855-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.355C>T(p.Pro119Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000161 in 1,613,924 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.355C>T | p.Pro119Ser | missense_variant | Exon 2 of 2 | 1 | NM_001013615.3 | ENSP00000361048.3 | ||
POMGNT1 | ENST00000371992.1 | c.-201G>A | 5_prime_UTR_variant | Exon 1 of 23 | 2 | ENSP00000361060.1 | ||||
POMGNT1 | ENST00000693223.1 | n.448G>A | non_coding_transcript_exon_variant | Exon 1 of 20 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152238Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 250138Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135288
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461686Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 727114
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152238Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74386
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.355C>T (p.P119S) 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 355, causing the proline (P) at amino acid position 119 to be replaced by a serine (S). 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