5-154713059-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_015315.6(LARP1):c.134C>T(p.Pro45Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000929 in 1,614,050 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015315.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LARP1 | XM_047417040.1 | c.-915C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 21 | XP_047272996.1 | |||
LARP1 | NM_015315.6 | c.134C>T | p.Pro45Leu | missense_variant | Exon 1 of 19 | NP_056130.2 | ||
LARP1 | NM_001367717.1 | c.134C>T | p.Pro45Leu | missense_variant | Exon 1 of 19 | NP_001354646.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LARP1 | ENST00000336314.9 | c.134C>T | p.Pro45Leu | missense_variant | Exon 1 of 19 | 1 | ENSP00000336721.4 | |||
LARP1 | ENST00000687700.1 | c.-180+30022C>T | intron_variant | Intron 1 of 18 | ENSP00000508958.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251192Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135786
GnomAD4 exome AF: 0.00000752 AC: 11AN: 1461878Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727244
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.134C>T (p.P45L) alteration is located in exon 1 (coding exon 1) of the LARP1 gene. This alteration results from a C to T substitution at nucleotide position 134, causing the proline (P) at amino acid position 45 to be replaced by a leucine (L). 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