rs72546327
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_198578.4(LRRK2):c.4229C>T(p.Thr1410Met) variant causes a missense change. The variant allele was found at a frequency of 0.00116 in 1,613,692 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. T1410T) has been classified as Likely benign.
Frequency
Consequence
NM_198578.4 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 | UniProt |
---|---|---|---|---|---|---|---|
LRRK2 | NM_198578.4 | c.4229C>T | p.Thr1410Met | missense_variant | 30/51 | ENST00000298910.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRK2 | ENST00000298910.12 | c.4229C>T | p.Thr1410Met | missense_variant | 30/51 | 1 | NM_198578.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00570 AC: 867AN: 151984Hom.: 7 Cov.: 32
GnomAD3 exomes AF: 0.00172 AC: 431AN: 251114Hom.: 5 AF XY: 0.00136 AC XY: 184AN XY: 135712
GnomAD4 exome AF: 0.000686 AC: 1002AN: 1461590Hom.: 11 Cov.: 34 AF XY: 0.000634 AC XY: 461AN XY: 727096
GnomAD4 genome ? AF: 0.00571 AC: 868AN: 152102Hom.: 7 Cov.: 32 AF XY: 0.00538 AC XY: 400AN XY: 74356
ClinVar
Submissions by phenotype
Autosomal dominant Parkinson disease 8 Benign:2Other:1
not provided, no classification provided | literature only | GeneReviews | - | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 23, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 02, 2020 | This variant is associated with the following publications: (PMID: 25821816, 24313877) - |
LRRK2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 18, 2022 | 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