rs41381646
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_024652.6(LRRK1):c.1896A>G(p.Lys632Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0125 in 1,614,202 control chromosomes in the GnomAD database, including 418 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_024652.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRRK1 | NM_024652.6 | c.1896A>G | p.Lys632Lys | synonymous_variant | Exon 15 of 34 | ENST00000388948.8 | NP_078928.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0332 AC: 5058AN: 152192Hom.: 186 Cov.: 32
GnomAD3 exomes AF: 0.0146 AC: 3632AN: 249578Hom.: 101 AF XY: 0.0131 AC XY: 1768AN XY: 135404
GnomAD4 exome AF: 0.0104 AC: 15154AN: 1461892Hom.: 230 Cov.: 32 AF XY: 0.0102 AC XY: 7405AN XY: 727248
GnomAD4 genome AF: 0.0334 AC: 5082AN: 152310Hom.: 188 Cov.: 32 AF XY: 0.0324 AC XY: 2414AN XY: 74492
ClinVar
Submissions by phenotype
not provided Benign:2
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LRRK1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at