chr2-127643047-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001161403.3(LIMS2):c.385C>T(p.Arg129Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00515 in 1,585,184 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R129G) has been classified as Uncertain significance.
Frequency
Consequence
NM_001161403.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIMS2 | NM_001161403.3 | c.385C>T | p.Arg129Cys | missense_variant | 5/10 | ENST00000355119.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIMS2 | ENST00000355119.9 | c.385C>T | p.Arg129Cys | missense_variant | 5/10 | 1 | NM_001161403.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00556 AC: 847AN: 152258Hom.: 2 Cov.: 34
GnomAD3 exomes AF: 0.00504 AC: 1017AN: 201794Hom.: 3 AF XY: 0.00513 AC XY: 557AN XY: 108576
GnomAD4 exome AF: 0.00510 AC: 7307AN: 1432808Hom.: 27 Cov.: 34 AF XY: 0.00521 AC XY: 3696AN XY: 710014
GnomAD4 genome AF: 0.00557 AC: 849AN: 152376Hom.: 2 Cov.: 34 AF XY: 0.00553 AC XY: 412AN XY: 74508
ClinVar
Submissions by phenotype
LIMS2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 10, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | LIMS2: BS2 - |
Autosomal recessive limb-girdle muscular dystrophy type 2W Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at