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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.


Current Build 155

Released April 9, 2021

Homo sapiens
chr1:778930 (GRCh38.p13) 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.

Variation Type
SNV Single Nucleotide Variation
G=0.030972 (4298/138770, GnomAD)
G=0.04494 (734/16332, ALFA)
G=0.0280 (108/3854, ALSPAC) (+ 6 more)
G=0.0256 (95/3708, TWINSUK)
G=0.0005 (1/1830, Korea1K)
G=0.011 (11/998, GoNL)
G=0.042 (9/216, Qatari)
C=0.50 (17/34, SGDP_PRJ)
G=0.50 (17/34, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01409 : Non Coding Transcript Variant
LOC100288069 : 2KB Upstream Variant
0 citations
Genomic View
See rs on genome

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.p13 chr 1 NC_000001.11:g.778930C>G
GRCh37.p13 chr 1 NC_000001.10:g.714310C>G
Gene: LOC100288069, uncharacterized LOC100288069 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
LOC100288069 transcript NR_168328.1:n. N/A Upstream Transcript Variant
Gene: LINC01409, uncharacterized LINC01409 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01409 transcript variant X4 XR_946806.3:n.189C>G N/A Non Coding Transcript Variant
LINC01409 transcript variant X5 XR_002958525.1:n.122C>G N/A Non Coding Transcript Variant
LINC01409 transcript variant X1 XR_002958522.1:n. N/A Genic Upstream Transcript Variant
LINC01409 transcript variant X2 XR_002958523.1:n. N/A Genic Upstream Transcript Variant
LINC01409 transcript variant X3 XR_002958524.1:n. N/A Genic Upstream Transcript 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

ALFA Allele Frequency (New)
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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 16332 C=0.95506 G=0.04494
European Sub 12080 C=0.94876 G=0.05124
African Sub 2816 C=0.9734 G=0.0266
African Others Sub 108 C=0.954 G=0.046
African American Sub 2708 C=0.9742 G=0.0258
Asian Sub 108 C=0.981 G=0.019
East Asian Sub 84 C=0.98 G=0.02
Other Asian Sub 24 C=1.00 G=0.00
Latin American 1 Sub 146 C=0.966 G=0.034
Latin American 2 Sub 610 C=0.984 G=0.016
South Asian Sub 94 C=0.95 G=0.05
Other Sub 478 C=0.962 G=0.038


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").

Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Genomes Global Study-wide 138770 C=0.969028 G=0.030972
gnomAD - Genomes European Sub 75092 C=0.96468 G=0.03532
gnomAD - Genomes African Sub 41608 C=0.97690 G=0.02310
gnomAD - Genomes American Sub 13564 C=0.97685 G=0.02315
gnomAD - Genomes Ashkenazi Jewish Sub 3246 C=0.9100 G=0.0900
gnomAD - Genomes East Asian Sub 3132 C=0.9974 G=0.0026
gnomAD - Genomes Other Sub 2128 C=0.9666 G=0.0334
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9720 G=0.0280
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9744 G=0.0256
Korean Genome Project KOREAN Study-wide 1830 C=0.9995 G=0.0005
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.989 G=0.011
Qatari Global Study-wide 216 C=0.958 G=0.042
SGDP_PRJ Global Study-wide 34 C=0.50 G=0.50

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 C= G
GRCh38.p13 chr 1 NC_000001.11:g.778930= NC_000001.11:g.778930C>G
GRCh37.p13 chr 1 NC_000001.10:g.714310= NC_000001.10:g.714310C>G
LINC01409 transcript variant X4 XR_946806.3:n.189= XR_946806.3:n.189C>G
LINC01409 transcript variant X5 XR_002958525.1:n.122= XR_002958525.1:n.122C>G

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#.

11 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss328357066 May 09, 2011 (134)
2 EVA-GONL ss974769041 Aug 21, 2014 (142)
3 EVA_UK10K_ALSPAC ss1599378227 Apr 01, 2015 (144)
4 EVA_UK10K_TWINSUK ss1642372260 Apr 01, 2015 (144)
5 WEILL_CORNELL_DGM ss1917959702 Feb 12, 2016 (147)
6 GNOMAD ss2750632786 Nov 08, 2017 (151)
7 SWEGEN ss2986147681 Nov 08, 2017 (151)
8 TOPMED ss3066388272 Nov 08, 2017 (151)
9 CSHL ss3343272170 Nov 08, 2017 (151)
10 SGDP_PRJ ss3847993772 Apr 25, 2020 (154)
11 KOGIC ss3943628314 Apr 25, 2020 (154)
12 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 714310 Oct 11, 2018 (152)
13 gnomAD - Genomes NC_000001.11 - 778930 Apr 25, 2021 (155)
14 Genome of the Netherlands Release 5 NC_000001.10 - 714310 Apr 25, 2020 (154)
15 Korean Genome Project NC_000001.11 - 778930 Apr 25, 2020 (154)
16 Qatari NC_000001.10 - 714310 Apr 25, 2020 (154)
17 SGDP_PRJ NC_000001.10 - 714310 Apr 25, 2020 (154)
18 UK 10K study - Twins NC_000001.10 - 714310 Oct 11, 2018 (152)
19 ALFA NC_000001.11 - 778930 Apr 25, 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
68, 161, 1632, 10752, 68, ss328357066, ss974769041, ss1599378227, ss1642372260, ss1917959702, ss2750632786, ss2986147681, ss3343272170, ss3847993772 NC_000001.10:714309:C:G NC_000001.11:778929:C:G (self)
53237, 6315, 13504241342, ss3066388272, ss3943628314 NC_000001.11:778929:C:G NC_000001.11:778929:C:G (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 rs141232927


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.post596+ae089ad