rs41319544
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_024652.6(LRRK1):āc.2487G>Cā(p.Val829=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 1,613,728 control chromosomes in the GnomAD database, including 15,621 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.12 ( 1217 hom., cov: 32)
Exomes š: 0.14 ( 14404 hom. )
Consequence
LRRK1
NM_024652.6 synonymous
NM_024652.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.204
Genes affected
LRRK1 (HGNC:18608): (leucine rich repeat kinase 1) This gene encodes a multi-domain protein that is a leucine-rich repeat kinase and a GDP/GTP binding protein. The encoded protein is thought to play a role in the regulation of bone mass. Mice lacking a similar gene showed severe osteopetrosis, increased bone mineralization and decreased bone resorption. [provided by RefSeq, Jan 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
Variant 15-101027342-G-C is Benign according to our data. Variant chr15-101027342-G-C is described in ClinVar as [Benign]. Clinvar id is 1655883.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.204 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRK1 | NM_024652.6 | c.2487G>C | p.Val829= | synonymous_variant | 18/34 | ENST00000388948.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRK1 | ENST00000388948.8 | c.2487G>C | p.Val829= | synonymous_variant | 18/34 | 5 | NM_024652.6 | P1 | |
LRRK1 | ENST00000525284.5 | c.*420G>C | 3_prime_UTR_variant, NMD_transcript_variant | 17/33 | 1 | ||||
LRRK1 | ENST00000531270.5 | c.*415G>C | 3_prime_UTR_variant, NMD_transcript_variant | 17/32 | 1 |
Frequencies
GnomAD3 genomes AF: 0.120 AC: 18327AN: 152118Hom.: 1217 Cov.: 32
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GnomAD3 exomes AF: 0.114 AC: 28355AN: 249140Hom.: 1864 AF XY: 0.116 AC XY: 15665AN XY: 135236
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GnomAD4 exome AF: 0.137 AC: 200063AN: 1461492Hom.: 14404 Cov.: 32 AF XY: 0.136 AC XY: 99079AN XY: 727028
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GnomAD4 genome AF: 0.120 AC: 18333AN: 152236Hom.: 1217 Cov.: 32 AF XY: 0.115 AC XY: 8529AN XY: 74444
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
LRRK1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 31, 2019 | 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). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at