rs10988
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_020117.11(LARS1):c.3263G>A(p.Arg1088Lys) variant causes a missense change. The variant allele was found at a frequency of 0.275 in 1,612,416 control chromosomes in the GnomAD database, including 64,821 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_020117.11 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LARS1 | NM_020117.11 | c.3263G>A | p.Arg1088Lys | missense_variant | 31/32 | ENST00000394434.7 | NP_064502.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LARS1 | ENST00000394434.7 | c.3263G>A | p.Arg1088Lys | missense_variant | 31/32 | 1 | NM_020117.11 | ENSP00000377954.2 |
Frequencies
GnomAD3 genomes AF: 0.225 AC: 34153AN: 151922Hom.: 4831 Cov.: 32
GnomAD3 exomes AF: 0.274 AC: 68704AN: 250466Hom.: 10920 AF XY: 0.265 AC XY: 35852AN XY: 135374
GnomAD4 exome AF: 0.280 AC: 408891AN: 1460380Hom.: 59976 Cov.: 33 AF XY: 0.276 AC XY: 200257AN XY: 726522
GnomAD4 genome AF: 0.225 AC: 34173AN: 152036Hom.: 4845 Cov.: 32 AF XY: 0.225 AC XY: 16748AN XY: 74296
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 29, 2013 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at