Name: rs117627419
Published: September 21, 2022
License: Open Access

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs117627419

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:40312795 (GRCh38.p14) Help
The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.
Alleles: T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.008795 (2328/264690, TOPMED)
C=0.009833 (1377/140034, GnomAD)
C=0.01329 (251/18890, ALFA) (+ 11 more)
C=0.0050 (32/6404, 1000G_30x)
C=0.0046 (23/5008, 1000G)
C=0.0214 (96/4480, Estonian)
C=0.0138 (53/3854, ALSPAC)
C=0.0124 (46/3708, TWINSUK)
C=0.016 (16/998, GoNL)
C=0.013 (8/600, NorthernSweden)
T=0.5 (3/6, Siberian)
C=0.5 (3/6, Siberian)
T=0.5 (2/4, SGDP_PRJ)
C=0.5 (2/4, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LRRK2 : Intron Variant
Publications: 0 citations
Genomic View: See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	18890	T=0.98671	C=0.01329
European	Sub	14286	T=0.98369	C=0.01631
African	Sub	2946	T=0.9990	C=0.0010
African Others	Sub	114	T=1.000	C=0.000
African American	Sub	2832	T=0.9989	C=0.0011
Asian	Sub	112	T=1.000	C=0.000
East Asian	Sub	86	T=1.00	C=0.00
Other Asian	Sub	26	T=1.00	C=0.00
Latin American 1	Sub	146	T=0.993	C=0.007
Latin American 2	Sub	610	T=0.989	C=0.011
South Asian	Sub	98	T=1.00	C=0.00
Other	Sub	692	T=0.990	C=0.010

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	T=0.991205	C=0.008795
gnomAD - Genomes	Global	Study-wide	140034	T=0.990167	C=0.009833
gnomAD - Genomes	European	Sub	75884	T=0.98556	C=0.01444
gnomAD - Genomes	African	Sub	41976	T=0.99757	C=0.00243
gnomAD - Genomes	American	Sub	13576	T=0.98858	C=0.01142
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.9991	C=0.0009
gnomAD - Genomes	East Asian	Sub	3126	T=1.0000	C=0.0000
gnomAD - Genomes	Other	Sub	2150	T=0.9902	C=0.0098
Allele Frequency Aggregator	Total	Global	18890	T=0.98671	C=0.01329
Allele Frequency Aggregator	European	Sub	14286	T=0.98369	C=0.01631
Allele Frequency Aggregator	African	Sub	2946	T=0.9990	C=0.0010
Allele Frequency Aggregator	Other	Sub	692	T=0.990	C=0.010
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.989	C=0.011
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.993	C=0.007
Allele Frequency Aggregator	Asian	Sub	112	T=1.000	C=0.000
Allele Frequency Aggregator	South Asian	Sub	98	T=1.00	C=0.00
1000Genomes_30x	Global	Study-wide	6404	T=0.9950	C=0.0050
1000Genomes_30x	African	Sub	1786	T=1.0000	C=0.0000
1000Genomes_30x	Europe	Sub	1266	T=0.9842	C=0.0158
1000Genomes_30x	South Asian	Sub	1202	T=1.0000	C=0.0000
1000Genomes_30x	East Asian	Sub	1170	T=1.0000	C=0.0000
1000Genomes_30x	American	Sub	980	T=0.988	C=0.012
1000Genomes	Global	Study-wide	5008	T=0.9954	C=0.0046
1000Genomes	African	Sub	1322	T=1.0000	C=0.0000
1000Genomes	East Asian	Sub	1008	T=1.0000	C=0.0000
1000Genomes	Europe	Sub	1006	T=0.9861	C=0.0139
1000Genomes	South Asian	Sub	978	T=1.000	C=0.000
1000Genomes	American	Sub	694	T=0.987	C=0.013
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9786	C=0.0214
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9862	C=0.0138
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9876	C=0.0124
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.984	C=0.016
Northern Sweden	ACPOP	Study-wide	600	T=0.987	C=0.013
Siberian	Global	Study-wide	6	T=0.5	C=0.5
SGDP_PRJ	Global	Study-wide	4	T=0.5	C=0.5

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements

Sequence name	Change
GRCh38.p14 chr 12	NC_000012.12:g.40312795T>C
GRCh37.p13 chr 12	NC_000012.11:g.40706597T>C
LRRK2 RefSeqGene	NG_011709.1:g.92785T>C

Gene: LRRK2, leucine rich repeat kinase 2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LRRK2 transcript	NM_198578.4:c.4537-1177T>C	N/A	Intron Variant
LRRK2 transcript variant X1	XM_005268629.5:c.4537-117… XM_005268629.5:c.4537-1177T>C	N/A	Intron Variant
LRRK2 transcript variant X2	XM_011537877.4:c.4537-117… XM_011537877.4:c.4537-1177T>C	N/A	Intron Variant
LRRK2 transcript variant X8	XM_011537881.4:c.4537-117… XM_011537881.4:c.4537-1177T>C	N/A	Intron Variant
LRRK2 transcript variant X9	XM_017018786.3:c.4536+214… XM_017018786.3:c.4536+2146T>C	N/A	Intron Variant
LRRK2 transcript variant X10	XM_017018787.2:c.1453-117… XM_017018787.2:c.1453-1177T>C	N/A	Intron Variant
LRRK2 transcript variant X6	XM_024448833.2:c.3334-117… XM_024448833.2:c.3334-1177T>C	N/A	Intron Variant
LRRK2 transcript variant X3	XM_047428277.1:c.4537-117… XM_047428277.1:c.4537-1177T>C	N/A	Intron Variant
LRRK2 transcript variant X5	XM_047428278.1:c.4537-117… XM_047428278.1:c.4537-1177T>C	N/A	Intron Variant
LRRK2 transcript variant X7	XM_047428279.1:c.4537-117… XM_047428279.1:c.4537-1177T>C	N/A	Intron Variant
LRRK2 transcript variant X11	XM_011537882.4:c.	N/A	Genic Downstream Transcript Variant
LRRK2 transcript variant X4	XR_007063041.1:n.	N/A	Intron Variant

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement	T=	C
GRCh38.p14 chr 12	NC_000012.12:g.40312795=	NC_000012.12:g.40312795T>C
GRCh37.p13 chr 12	NC_000012.11:g.40706597=	NC_000012.11:g.40706597T>C
LRRK2 RefSeqGene	NG_011709.1:g.92785=	NG_011709.1:g.92785T>C
LRRK2 transcript	NM_198578.3:c.4537-1177=	NM_198578.3:c.4537-1177T>C
LRRK2 transcript	NM_198578.4:c.4537-1177=	NM_198578.4:c.4537-1177T>C
LRRK2 transcript variant X1	XM_005268629.1:c.4537-1177=	XM_005268629.1:c.4537-1177T>C
LRRK2 transcript variant X1	XM_005268629.5:c.4537-1177=	XM_005268629.5:c.4537-1177T>C
LRRK2 transcript variant X2	XM_005268630.1:c.4537-1177=	XM_005268630.1:c.4537-1177T>C
LRRK2 transcript variant X3	XM_005268631.1:c.4417-1177=	XM_005268631.1:c.4417-1177T>C
LRRK2 transcript variant X4	XM_005268632.1:c.4537-1177=	XM_005268632.1:c.4537-1177T>C
LRRK2 transcript variant X5	XM_005268633.1:c.4537-1177=	XM_005268633.1:c.4537-1177T>C
LRRK2 transcript variant X2	XM_011537877.4:c.4537-1177=	XM_011537877.4:c.4537-1177T>C
LRRK2 transcript variant X8	XM_011537881.4:c.4537-1177=	XM_011537881.4:c.4537-1177T>C
LRRK2 transcript variant X9	XM_017018786.3:c.4536+2146=	XM_017018786.3:c.4536+2146T>C
LRRK2 transcript variant X10	XM_017018787.2:c.1453-1177=	XM_017018787.2:c.1453-1177T>C
LRRK2 transcript variant X6	XM_024448833.2:c.3334-1177=	XM_024448833.2:c.3334-1177T>C
LRRK2 transcript variant X3	XM_047428277.1:c.4537-1177=	XM_047428277.1:c.4537-1177T>C
LRRK2 transcript variant X5	XM_047428278.1:c.4537-1177=	XM_047428278.1:c.4537-1177T>C
LRRK2 transcript variant X7	XM_047428279.1:c.4537-1177=	XM_047428279.1:c.4537-1177T>C

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

25 SubSNP, 12 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss235905706	Jul 15, 2010 (132)
2	EVA-GONL	ss989451907	Aug 21, 2014 (142)
3	JMKIDD_LAB	ss1078402541	Aug 21, 2014 (142)
4	1000GENOMES	ss1344701005	Aug 21, 2014 (142)
5	EVA_DECODE	ss1599119214	Apr 01, 2015 (144)
6	EVA_UK10K_ALSPAC	ss1628428394	Apr 01, 2015 (144)
7	EVA_UK10K_TWINSUK	ss1671422427	Apr 01, 2015 (144)
8	USC_VALOUEV	ss2155491454	Dec 20, 2016 (150)
9	HUMAN_LONGEVITY	ss2189137961	Dec 20, 2016 (150)
10	GNOMAD	ss2909599799	Nov 08, 2017 (151)
11	SWEGEN	ss3009554904	Nov 08, 2017 (151)
12	CSHL	ss3350027542	Nov 08, 2017 (151)
13	EGCUT_WGS	ss3676830501	Jul 13, 2019 (153)
14	EVA_DECODE	ss3693516311	Jul 13, 2019 (153)
15	ACPOP	ss3738951293	Jul 13, 2019 (153)
16	SGDP_PRJ	ss3878110627	Apr 27, 2020 (154)
17	TOPMED	ss4915526474	Apr 26, 2021 (155)
18	1000G_HIGH_COVERAGE	ss5290530458	Oct 16, 2022 (156)
19	EVA	ss5405140169	Oct 16, 2022 (156)
20	HUGCELL_USP	ss5485318541	Oct 16, 2022 (156)
21	1000G_HIGH_COVERAGE	ss5587881162	Oct 16, 2022 (156)
22	SANFORD_IMAGENETICS	ss5652996115	Oct 16, 2022 (156)
23	EVA	ss5837861555	Oct 16, 2022 (156)
24	EVA	ss5904077274	Oct 16, 2022 (156)
25	EVA	ss5944353749	Oct 16, 2022 (156)
26	1000Genomes	NC_000012.11 - 40706597	Oct 12, 2018 (152)
27	1000Genomes_30x	NC_000012.12 - 40312795	Oct 16, 2022 (156)
28	The Avon Longitudinal Study of Parents and Children	NC_000012.11 - 40706597	Oct 12, 2018 (152)
29	Genetic variation in the Estonian population	NC_000012.11 - 40706597	Oct 12, 2018 (152)
30	gnomAD - Genomes	NC_000012.12 - 40312795	Apr 26, 2021 (155)
31	Genome of the Netherlands Release 5	NC_000012.11 - 40706597	Apr 27, 2020 (154)
32	Northern Sweden	NC_000012.11 - 40706597	Jul 13, 2019 (153)
33	SGDP_PRJ	NC_000012.11 - 40706597	Apr 27, 2020 (154)
34	Siberian	NC_000012.11 - 40706597	Apr 27, 2020 (154)
35	TopMed	NC_000012.12 - 40312795	Apr 26, 2021 (155)
36	UK 10K study - Twins	NC_000012.11 - 40706597	Oct 12, 2018 (152)
37	ALFA	NC_000012.12 - 40312795	Apr 26, 2021 (155)

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss1599119214	NC_000012.10:38992863:T:C	NC_000012.12:40312794:T:C	(self)
57438070, 31895670, 22568749, 14234639, 12236158, 30127607, 8007808, 31895670, ss235905706, ss989451907, ss1078402541, ss1344701005, ss1628428394, ss1671422427, ss2155491454, ss2909599799, ss3009554904, ss3350027542, ss3676830501, ss3738951293, ss3878110627, ss5405140169, ss5652996115, ss5837861555, ss5944353749	NC_000012.11:40706596:T:C	NC_000012.12:40312794:T:C	(self)
75407097, 405036308, 131072131, 2308725085, ss2189137961, ss3693516311, ss4915526474, ss5290530458, ss5485318541, ss5587881162, ss5904077274	NC_000012.12:40312794:T:C	NC_000012.12:40312794:T:C	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs117627419

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:

Select flank length:

Genomic regions, transcripts, and products
Top▲ Help
NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs117627419