rs34778348
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The NM_198578.4(LRRK2):c.7153G>A(p.Gly2385Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000787 in 1,611,766 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity,risk factor (no stars). Synonymous variant affecting the same amino acid position (i.e. G2385G) 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 -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRK2 | NM_198578.4 | c.7153G>A | p.Gly2385Arg | missense_variant | 48/51 | ENST00000298910.12 | |
LOC105369736 | XR_944868.3 | n.485-8699C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRK2 | ENST00000298910.12 | c.7153G>A | p.Gly2385Arg | missense_variant | 48/51 | 1 | NM_198578.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000823 AC: 125AN: 151846Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00171 AC: 429AN: 250734Hom.: 7 AF XY: 0.00170 AC XY: 231AN XY: 135518
GnomAD4 exome AF: 0.000782 AC: 1142AN: 1459802Hom.: 22 Cov.: 33 AF XY: 0.000819 AC XY: 595AN XY: 726230
GnomAD4 genome ? AF: 0.000836 AC: 127AN: 151964Hom.: 5 Cov.: 32 AF XY: 0.00102 AC XY: 76AN XY: 74286
ClinVar
Submissions by phenotype
Autosomal dominant Parkinson disease 8 Pathogenic:1Uncertain:1Benign:2Other:2
risk factor, no assertion criteria provided | literature only | OMIM | Oct 01, 2008 | - - |
not provided, no classification provided | literature only | GeneReviews | - | - - |
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. - |
Pathogenic, flagged submission | provider interpretation | Codex Genetics Limited | Feb 28, 2019 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Apr 09, 2020 | - - |
Parkinson disease Other:1
risk factor, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Sep 21, 2020 | proposed classification - variant undergoing re-assessment, contact laboratory - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at