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dbSNP Short Genetic Variations

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.

rs750667752

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr15:101056935 (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
A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000004 (1/264690, TOPMED)
T=0.000020 (5/249288, GnomAD_exome)
T=0.000008 (1/120598, ExAC) (+ 1 more)
T=0.00000 (0/10680, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LRRK1 : Stop Gained
LOC105371026 : 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 10680 A=1.00000 T=0.00000
European Sub 6962 A=1.0000 T=0.0000
African Sub 2294 A=1.0000 T=0.0000
African Others Sub 84 A=1.00 T=0.00
African American Sub 2210 A=1.0000 T=0.0000
Asian Sub 108 A=1.000 T=0.000
East Asian Sub 84 A=1.00 T=0.00
Other Asian Sub 24 A=1.00 T=0.00
Latin American 1 Sub 146 A=1.000 T=0.000
Latin American 2 Sub 610 A=1.000 T=0.000
South Asian Sub 94 A=1.00 T=0.00
Other Sub 466 A=1.000 T=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 A=0.999996 T=0.000004
gnomAD - Exomes Global Study-wide 249288 A=0.999980 T=0.000020
gnomAD - Exomes European Sub 134644 A=1.000000 T=0.000000
gnomAD - Exomes Asian Sub 48564 A=1.00000 T=0.00000
gnomAD - Exomes American Sub 34490 A=0.99986 T=0.00014
gnomAD - Exomes African Sub 15478 A=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10060 A=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6052 A=1.0000 T=0.0000
ExAC Global Study-wide 120598 A=0.999992 T=0.000008
ExAC Europe Sub 73248 A=1.00000 T=0.00000
ExAC Asian Sub 25094 A=1.00000 T=0.00000
ExAC American Sub 11570 A=0.99991 T=0.00009
ExAC African Sub 9790 A=1.0000 T=0.0000
ExAC Other Sub 896 A=1.000 T=0.000
Allele Frequency Aggregator Total Global 10680 A=1.00000 T=0.00000
Allele Frequency Aggregator European Sub 6962 A=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 2294 A=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 A=1.000 T=0.000
Allele Frequency Aggregator Other Sub 466 A=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 A=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 108 A=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 94 A=1.00 T=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 15 NC_000015.10:g.101056935A>T
GRCh37.p13 chr 15 NC_000015.9:g.101597140A>T
LRRK1 RefSeqGene NG_052791.1:g.142919A>T
Gene: LRRK1, leucine rich repeat kinase 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LRRK1 transcript NM_024652.6:c.4412A>T Q [CAG] > L [CTG] Coding Sequence Variant
leucine-rich repeat serine/threonine-protein kinase 1 NP_078928.3:p.Gln1471Leu Q (Gln) > L (Leu) Missense Variant
LRRK1 transcript variant X2 XM_047433035.1:c. N/A Genic Downstream Transcript Variant
LRRK1 transcript variant X1 XM_047433034.1:c.4408A>T R [AGA] > * [TGA] Coding Sequence Variant
leucine-rich repeat serine/threonine-protein kinase 1 isoform X1 XP_047288990.1:p.Arg1470T…

XP_047288990.1:p.Arg1470Ter

R (Arg) > * (Ter) Stop Gained
Gene: LOC105371026, uncharacterized LOC105371026 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105371026 transcript variant X1 XR_001751721.2:n. N/A Intron Variant
LOC105371026 transcript variant X6 XR_001751723.2:n. N/A Intron Variant
LOC105371026 transcript variant X8 XR_001751724.2:n. N/A Intron Variant
LOC105371026 transcript variant X3 XR_001751725.2:n. N/A Intron Variant
LOC105371026 transcript variant X4 XR_001751726.2:n. N/A Intron Variant
LOC105371026 transcript variant X5 XR_001751727.2:n. N/A Intron Variant
LOC105371026 transcript variant X2 XR_932737.3:n. N/A Intron Variant
LOC105371026 transcript variant X7 XR_007064779.1:n. N/A Genic Upstream 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 A= T
GRCh38.p14 chr 15 NC_000015.10:g.101056935= NC_000015.10:g.101056935A>T
GRCh37.p13 chr 15 NC_000015.9:g.101597140= NC_000015.9:g.101597140A>T
LRRK1 RefSeqGene NG_052791.1:g.142919= NG_052791.1:g.142919A>T
LRRK1 transcript NM_024652.6:c.4412= NM_024652.6:c.4412A>T
LRRK1 transcript NM_024652.5:c.4412= NM_024652.5:c.4412A>T
LRRK1 transcript NM_024652.4:c.4412= NM_024652.4:c.4412A>T
LRRK1 transcript NM_024652.3:c.4412= NM_024652.3:c.4412A>T
LRRK1 transcript variant X1 XM_047433034.1:c.4408= XM_047433034.1:c.4408A>T
leucine-rich repeat serine/threonine-protein kinase 1 NP_078928.3:p.Gln1471= NP_078928.3:p.Gln1471Leu
leucine-rich repeat serine/threonine-protein kinase 1 isoform X1 XP_047288990.1:p.Arg1470= XP_047288990.1:p.Arg1470Ter
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#.

3 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1692021278 Apr 01, 2015 (144)
2 GNOMAD ss2741546853 Nov 08, 2017 (151)
3 TOPMED ss5004001061 Apr 26, 2021 (155)
4 ExAC NC_000015.9 - 101597140 Oct 12, 2018 (152)
5 gnomAD - Exomes NC_000015.9 - 101597140 Jul 13, 2019 (153)
6 TopMed NC_000015.10 - 101056935 Apr 26, 2021 (155)
7 ALFA NC_000015.10 - 101056935 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
2409355, 10817678, ss1692021278, ss2741546853 NC_000015.9:101597139:A:T NC_000015.10:101056934:A:T (self)
219546721, 6496129489, ss5004001061 NC_000015.10:101056934:A:T NC_000015.10:101056934:A:T (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 rs750667752

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