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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs200789262

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr12:40232368 (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>A / T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000008 (2/264690, TOPMED)
C=0.000020 (5/251416, GnomAD_exome)
C=0.000033 (4/121316, ExAC) (+ 1 more)
C=0.00000 (0/14420, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LRRK2 : Missense 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 14420 T=1.00000 C=0.00000
European Sub 9824 T=1.0000 C=0.0000
African Sub 2946 T=1.0000 C=0.0000
African Others Sub 114 T=1.000 C=0.000
African American Sub 2832 T=1.0000 C=0.0000
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=1.000 C=0.000
Latin American 2 Sub 610 T=1.000 C=0.000
South Asian Sub 98 T=1.00 C=0.00
Other Sub 684 T=1.000 C=0.000


Help

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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 T=0.999992 C=0.000008
gnomAD - Exomes Global Study-wide 251416 T=0.999980 C=0.000020
gnomAD - Exomes European Sub 135350 T=0.999963 C=0.000037
gnomAD - Exomes Asian Sub 49010 T=1.00000 C=0.00000
gnomAD - Exomes American Sub 34586 T=1.00000 C=0.00000
gnomAD - Exomes African Sub 16256 T=1.00000 C=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10076 T=1.00000 C=0.00000
gnomAD - Exomes Other Sub 6138 T=1.0000 C=0.0000
ExAC Global Study-wide 121316 T=0.999967 C=0.000033
ExAC Europe Sub 73294 T=0.99995 C=0.00005
ExAC Asian Sub 25156 T=1.00000 C=0.00000
ExAC American Sub 11560 T=1.00000 C=0.00000
ExAC African Sub 10402 T=1.00000 C=0.00000
ExAC Other Sub 904 T=1.000 C=0.000
Allele Frequency Aggregator Total Global 14420 T=1.00000 C=0.00000
Allele Frequency Aggregator European Sub 9824 T=1.0000 C=0.0000
Allele Frequency Aggregator African Sub 2946 T=1.0000 C=0.0000
Allele Frequency Aggregator Other Sub 684 T=1.000 C=0.000
Allele Frequency Aggregator Latin American 2 Sub 610 T=1.000 C=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 T=1.000 C=0.000
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
Help

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.40232368T>A
GRCh38.p14 chr 12 NC_000012.12:g.40232368T>C
GRCh37.p13 chr 12 NC_000012.11:g.40626170T>A
GRCh37.p13 chr 12 NC_000012.11:g.40626170T>C
LRRK2 RefSeqGene NG_011709.1:g.12358T>A
LRRK2 RefSeqGene NG_011709.1:g.12358T>C
Gene: LRRK2, leucine rich repeat kinase 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LRRK2 transcript NM_198578.4:c.332T>A V [GTC] > D [GAC] Coding Sequence Variant
leucine-rich repeat serine/threonine-protein kinase 2 NP_940980.4:p.Val111Asp V (Val) > D (Asp) Missense Variant
LRRK2 transcript NM_198578.4:c.332T>C V [GTC] > A [GCC] Coding Sequence Variant
leucine-rich repeat serine/threonine-protein kinase 2 NP_940980.4:p.Val111Ala V (Val) > A (Ala) Missense Variant
LRRK2 transcript variant X10 XM_017018787.2:c. N/A Genic Upstream Transcript Variant
LRRK2 transcript variant X6 XM_024448833.2:c. N/A Genic Upstream Transcript Variant
LRRK2 transcript variant X1 XM_005268629.5:c.332T>A V [GTC] > D [GAC] Coding Sequence Variant
leucine-rich repeat serine/threonine-protein kinase 2 isoform X1 XP_005268686.1:p.Val111Asp V (Val) > D (Asp) Missense Variant
LRRK2 transcript variant X1 XM_005268629.5:c.332T>C V [GTC] > A [GCC] Coding Sequence Variant
leucine-rich repeat serine/threonine-protein kinase 2 isoform X1 XP_005268686.1:p.Val111Ala V (Val) > A (Ala) Missense Variant
LRRK2 transcript variant X2 XM_011537877.4:c.332T>A V [GTC] > D [GAC] Coding Sequence Variant
leucine-rich repeat serine/threonine-protein kinase 2 isoform X2 XP_011536179.1:p.Val111Asp V (Val) > D (Asp) Missense Variant
LRRK2 transcript variant X2 XM_011537877.4:c.332T>C V [GTC] > A [GCC] Coding Sequence Variant
leucine-rich repeat serine/threonine-protein kinase 2 isoform X2 XP_011536179.1:p.Val111Ala V (Val) > A (Ala) Missense Variant
LRRK2 transcript variant X3 XM_047428277.1:c.332T>A V [GTC] > D [GAC] Coding Sequence Variant
leucine-rich repeat serine/threonine-protein kinase 2 isoform X3 XP_047284233.1:p.Val111Asp V (Val) > D (Asp) Missense Variant
LRRK2 transcript variant X3 XM_047428277.1:c.332T>C V [GTC] > A [GCC] Coding Sequence Variant
leucine-rich repeat serine/threonine-protein kinase 2 isoform X3 XP_047284233.1:p.Val111Ala V (Val) > A (Ala) Missense Variant
LRRK2 transcript variant X5 XM_047428278.1:c.332T>A V [GTC] > D [GAC] Coding Sequence Variant
leucine-rich repeat serine/threonine-protein kinase 2 isoform X4 XP_047284234.1:p.Val111Asp V (Val) > D (Asp) Missense Variant
LRRK2 transcript variant X5 XM_047428278.1:c.332T>C V [GTC] > A [GCC] Coding Sequence Variant
leucine-rich repeat serine/threonine-protein kinase 2 isoform X4 XP_047284234.1:p.Val111Ala V (Val) > A (Ala) Missense Variant
LRRK2 transcript variant X7 XM_047428279.1:c.332T>A V [GTC] > D [GAC] Coding Sequence Variant
leucine-rich repeat serine/threonine-protein kinase 2 isoform X6 XP_047284235.1:p.Val111Asp V (Val) > D (Asp) Missense Variant
LRRK2 transcript variant X7 XM_047428279.1:c.332T>C V [GTC] > A [GCC] Coding Sequence Variant
leucine-rich repeat serine/threonine-protein kinase 2 isoform X6 XP_047284235.1:p.Val111Ala V (Val) > A (Ala) Missense Variant
LRRK2 transcript variant X8 XM_011537881.4:c.332T>A V [GTC] > D [GAC] Coding Sequence Variant
leucine-rich repeat serine/threonine-protein kinase 2 isoform X7 XP_011536183.1:p.Val111Asp V (Val) > D (Asp) Missense Variant
LRRK2 transcript variant X8 XM_011537881.4:c.332T>C V [GTC] > A [GCC] Coding Sequence Variant
leucine-rich repeat serine/threonine-protein kinase 2 isoform X7 XP_011536183.1:p.Val111Ala V (Val) > A (Ala) Missense Variant
LRRK2 transcript variant X9 XM_017018786.3:c.332T>A V [GTC] > D [GAC] Coding Sequence Variant
leucine-rich repeat serine/threonine-protein kinase 2 isoform X8 XP_016874275.1:p.Val111Asp V (Val) > D (Asp) Missense Variant
LRRK2 transcript variant X9 XM_017018786.3:c.332T>C V [GTC] > A [GCC] Coding Sequence Variant
leucine-rich repeat serine/threonine-protein kinase 2 isoform X8 XP_016874275.1:p.Val111Ala V (Val) > A (Ala) Missense Variant
LRRK2 transcript variant X11 XM_011537882.4:c.332T>A V [GTC] > D [GAC] Coding Sequence Variant
leucine-rich repeat serine/threonine-protein kinase 2 isoform X10 XP_011536184.1:p.Val111Asp V (Val) > D (Asp) Missense Variant
LRRK2 transcript variant X11 XM_011537882.4:c.332T>C V [GTC] > A [GCC] Coding Sequence Variant
leucine-rich repeat serine/threonine-protein kinase 2 isoform X10 XP_011536184.1:p.Val111Ala V (Val) > A (Ala) Missense Variant
LRRK2 transcript variant X4 XR_007063041.1:n.467T>A N/A Non Coding Transcript Variant
LRRK2 transcript variant X4 XR_007063041.1:n.467T>C N/A Non Coding Transcript Variant
Help

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
Help

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= A C
GRCh38.p14 chr 12 NC_000012.12:g.40232368= NC_000012.12:g.40232368T>A NC_000012.12:g.40232368T>C
GRCh37.p13 chr 12 NC_000012.11:g.40626170= NC_000012.11:g.40626170T>A NC_000012.11:g.40626170T>C
LRRK2 RefSeqGene NG_011709.1:g.12358= NG_011709.1:g.12358T>A NG_011709.1:g.12358T>C
LRRK2 transcript NM_198578.4:c.332= NM_198578.4:c.332T>A NM_198578.4:c.332T>C
LRRK2 transcript NM_198578.3:c.332= NM_198578.3:c.332T>A NM_198578.3:c.332T>C
LRRK2 transcript variant X1 XM_005268629.5:c.332= XM_005268629.5:c.332T>A XM_005268629.5:c.332T>C
LRRK2 transcript variant X1 XM_005268629.4:c.332= XM_005268629.4:c.332T>A XM_005268629.4:c.332T>C
LRRK2 transcript variant X1 XM_005268629.3:c.332= XM_005268629.3:c.332T>A XM_005268629.3:c.332T>C
LRRK2 transcript variant X1 XM_005268629.2:c.332= XM_005268629.2:c.332T>A XM_005268629.2:c.332T>C
LRRK2 transcript variant X1 XM_005268629.1:c.332= XM_005268629.1:c.332T>A XM_005268629.1:c.332T>C
LRRK2 transcript variant X2 XM_011537877.4:c.332= XM_011537877.4:c.332T>A XM_011537877.4:c.332T>C
LRRK2 transcript variant X2 XM_011537877.3:c.332= XM_011537877.3:c.332T>A XM_011537877.3:c.332T>C
LRRK2 transcript variant X2 XM_011537877.2:c.332= XM_011537877.2:c.332T>A XM_011537877.2:c.332T>C
LRRK2 transcript variant X2 XM_011537877.1:c.332= XM_011537877.1:c.332T>A XM_011537877.1:c.332T>C
LRRK2 transcript variant X8 XM_011537881.4:c.332= XM_011537881.4:c.332T>A XM_011537881.4:c.332T>C
LRRK2 transcript variant X5 XM_011537881.3:c.332= XM_011537881.3:c.332T>A XM_011537881.3:c.332T>C
LRRK2 transcript variant X4 XM_011537881.2:c.332= XM_011537881.2:c.332T>A XM_011537881.2:c.332T>C
LRRK2 transcript variant X6 XM_011537881.1:c.332= XM_011537881.1:c.332T>A XM_011537881.1:c.332T>C
LRRK2 transcript variant X11 XM_011537882.4:c.332= XM_011537882.4:c.332T>A XM_011537882.4:c.332T>C
LRRK2 transcript variant X9 XM_011537882.3:c.332= XM_011537882.3:c.332T>A XM_011537882.3:c.332T>C
LRRK2 transcript variant X8 XM_011537882.2:c.332= XM_011537882.2:c.332T>A XM_011537882.2:c.332T>C
LRRK2 transcript variant X7 XM_011537882.1:c.332= XM_011537882.1:c.332T>A XM_011537882.1:c.332T>C
LRRK2 transcript variant X9 XM_017018786.3:c.332= XM_017018786.3:c.332T>A XM_017018786.3:c.332T>C
LRRK2 transcript variant X6 XM_017018786.2:c.332= XM_017018786.2:c.332T>A XM_017018786.2:c.332T>C
LRRK2 transcript variant X5 XM_017018786.1:c.332= XM_017018786.1:c.332T>A XM_017018786.1:c.332T>C
LRRK2 transcript variant X4 XR_007063041.1:n.467= XR_007063041.1:n.467T>A XR_007063041.1:n.467T>C
LRRK2 transcript variant X3 XM_047428277.1:c.332= XM_047428277.1:c.332T>A XM_047428277.1:c.332T>C
LRRK2 transcript variant X5 XM_047428278.1:c.332= XM_047428278.1:c.332T>A XM_047428278.1:c.332T>C
LRRK2 transcript variant X7 XM_047428279.1:c.332= XM_047428279.1:c.332T>A XM_047428279.1:c.332T>C
leucine-rich repeat serine/threonine-protein kinase 2 NP_940980.4:p.Val111= NP_940980.4:p.Val111Asp NP_940980.4:p.Val111Ala
leucine-rich repeat serine/threonine-protein kinase 2 isoform X1 XP_005268686.1:p.Val111= XP_005268686.1:p.Val111Asp XP_005268686.1:p.Val111Ala
leucine-rich repeat serine/threonine-protein kinase 2 isoform X2 XP_011536179.1:p.Val111= XP_011536179.1:p.Val111Asp XP_011536179.1:p.Val111Ala
leucine-rich repeat serine/threonine-protein kinase 2 isoform X7 XP_011536183.1:p.Val111= XP_011536183.1:p.Val111Asp XP_011536183.1:p.Val111Ala
leucine-rich repeat serine/threonine-protein kinase 2 isoform X10 XP_011536184.1:p.Val111= XP_011536184.1:p.Val111Asp XP_011536184.1:p.Val111Ala
leucine-rich repeat serine/threonine-protein kinase 2 isoform X8 XP_016874275.1:p.Val111= XP_016874275.1:p.Val111Asp XP_016874275.1:p.Val111Ala
leucine-rich repeat serine/threonine-protein kinase 2 isoform X3 XP_047284233.1:p.Val111= XP_047284233.1:p.Val111Asp XP_047284233.1:p.Val111Ala
leucine-rich repeat serine/threonine-protein kinase 2 isoform X4 XP_047284234.1:p.Val111= XP_047284234.1:p.Val111Asp XP_047284234.1:p.Val111Ala
leucine-rich repeat serine/threonine-protein kinase 2 isoform X6 XP_047284235.1:p.Val111= XP_047284235.1:p.Val111Asp XP_047284235.1:p.Val111Ala
leucine-rich repeat serine/threonine-protein kinase 2 NP_940980.3:p.Val111= NP_940980.3:p.Val111Asp NP_940980.3:p.Val111Ala
Help

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#.

5 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 GSK-GENETICS ss475884344 May 04, 2012 (137)
2 EVA_EXAC ss1690853646 Apr 01, 2015 (144)
3 GNOMAD ss2739729759 Nov 08, 2017 (151)
4 TOPMED ss4915507291 Apr 26, 2021 (155)
5 EVA ss5799446985 Oct 16, 2022 (156)
6 ExAC NC_000012.11 - 40626170 Oct 12, 2018 (152)
7 gnomAD - Exomes NC_000012.11 - 40626170 Jul 13, 2019 (153)
8 TopMed NC_000012.12 - 40232368 Apr 26, 2021 (155)
9 ALFA NC_000012.12 - 40232368 Apr 26, 2021 (155)
Help

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
ss5799446985 NC_000012.11:40626169:T:A NC_000012.12:40232367:T:A
ss475884344 NC_000012.10:38912436:T:C NC_000012.12:40232367:T:C (self)
1146941, 8958754, ss1690853646, ss2739729759 NC_000012.11:40626169:T:C NC_000012.12:40232367:T:C (self)
131052948, 11950320943, ss4915507291 NC_000012.12:40232367:T:C NC_000012.12:40232367:T:C (self)
Help

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

No publications for rs200789262

Help

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.

Software version is: 2.0.1.post761+d5e8e07