rs11176143
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_198578.4(LRRK2):c.6381+52G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.088 in 1,055,146 control chromosomes in the GnomAD database, including 5,549 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.083 ( 703 hom., cov: 32)
Exomes 𝑓: 0.089 ( 4846 hom. )
Consequence
LRRK2
NM_198578.4 intron
NM_198578.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.16
Genes affected
LRRK2 (HGNC:18618): (leucine rich repeat kinase 2) This gene is a member of the leucine-rich repeat kinase family and encodes a protein with an ankryin repeat region, a leucine-rich repeat (LRR) domain, a kinase domain, a DFG-like motif, a RAS domain, a GTPase domain, a MLK-like domain, and a WD40 domain. The protein is present largely in the cytoplasm but also associates with the mitochondrial outer membrane. Mutations in this gene have been associated with Parkinson disease-8. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BP6
?
Variant 12-40348561-G-A is Benign according to our data. Variant chr12-40348561-G-A is described in ClinVar as [Benign]. Clinvar id is 1238322.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRK2 | NM_198578.4 | c.6381+52G>A | intron_variant | ENST00000298910.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRK2 | ENST00000298910.12 | c.6381+52G>A | intron_variant | 1 | NM_198578.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0830 AC: 12606AN: 151906Hom.: 704 Cov.: 32
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GnomAD3 exomes AF: 0.0969 AC: 18460AN: 190470Hom.: 1189 AF XY: 0.101 AC XY: 10322AN XY: 102234
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GnomAD4 exome AF: 0.0889 AC: 80300AN: 903122Hom.: 4846 Cov.: 12 AF XY: 0.0934 AC XY: 43700AN XY: 468090
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GnomAD4 genome ? AF: 0.0829 AC: 12598AN: 152024Hom.: 703 Cov.: 32 AF XY: 0.0862 AC XY: 6406AN XY: 74300
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 21, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at