5-154793949-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_033551.3(LARP1):c.1018C>T(p.Arg340Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,613,208 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_033551.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LARP1 | NM_033551.3 | c.1018C>T | p.Arg340Cys | missense_variant | Exon 6 of 19 | ENST00000518297.6 | NP_291029.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LARP1 | ENST00000518297.6 | c.1018C>T | p.Arg340Cys | missense_variant | Exon 6 of 19 | 5 | NM_033551.3 | ENSP00000428589.2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249338Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134998
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461030Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 726720
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.787C>T (p.R263C) alteration is located in exon 6 (coding exon 6) of the LARP1 gene. This alteration results from a C to T substitution at nucleotide position 787, causing the arginine (R) at amino acid position 263 to be replaced by a cysteine (C). 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