chr5-154794157-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_033551.3(LARP1):c.1127C>T(p.Thr376Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00109 in 1,614,040 control chromosomes in the GnomAD database, including 2 homozygotes. 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_033551.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LARP1 | NM_033551.3 | c.1127C>T | p.Thr376Met | missense_variant | Exon 7 of 19 | ENST00000518297.6 | NP_291029.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LARP1 | ENST00000518297.6 | c.1127C>T | p.Thr376Met | missense_variant | Exon 7 of 19 | 5 | NM_033551.3 | ENSP00000428589.2 |
Frequencies
GnomAD3 genomes AF: 0.000743 AC: 113AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000585 AC: 147AN: 251488Hom.: 0 AF XY: 0.000611 AC XY: 83AN XY: 135914
GnomAD4 exome AF: 0.00113 AC: 1652AN: 1461882Hom.: 2 Cov.: 31 AF XY: 0.00110 AC XY: 798AN XY: 727246
GnomAD4 genome AF: 0.000743 AC: 113AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.000659 AC XY: 49AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.896C>T (p.T299M) alteration is located in exon 7 (coding exon 7) of the LARP1 gene. This alteration results from a C to T substitution at nucleotide position 896, causing the threonine (T) at amino acid position 299 to be replaced by a methionine (M). 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