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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
chr1:843931-843938 (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
Indel Insertion and Deletion
delGA=0.020171 (5339/264690, TOPMED)
delGA=0.012558 (1761/140228, GnomAD)
delGA=0.00724 (134/18520, ALFA) (+ 6 more)
delGA=0.15447 (2589/16760, 8.3KJPN)
delGA=0.0453 (227/5008, 1000G)
delGA=0.0013 (5/3854, ALSPAC)
delGA=0.0005 (2/3708, TWINSUK)
delGA=0.1517 (278/1832, Korea1K)
delGA=0.167 (36/216, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01128 : Intron 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.843931GA[3]
GRCh37.p13 chr 1 NC_000001.10:g.779311GA[3]
Gene: LINC01128, long intergenic non-protein coding RNA 1128 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01128 transcript variant 1 NR_047519.1:n. N/A Intron Variant
LINC01128 transcript variant 3 NR_047521.1:n. N/A Intron Variant
LINC01128 transcript variant 5 NR_047523.1:n. N/A Intron Variant
LINC01128 transcript variant 7 NR_047524.1:n. N/A Intron Variant
LINC01128 transcript variant 8 NR_047525.1:n. N/A Intron Variant
LINC01128 transcript variant 9 NR_047526.1:n. N/A Genic Downstream 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
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 18520 GAGAGAGA=0.99276 GAGAGA=0.00724
European Sub 14152 GAGAGAGA=0.99809 GAGAGA=0.00191
African Sub 2898 GAGAGAGA=0.9907 GAGAGA=0.0093
African Others Sub 114 GAGAGAGA=0.991 GAGAGA=0.009
African American Sub 2784 GAGAGAGA=0.9907 GAGAGA=0.0093
Asian Sub 112 GAGAGAGA=0.884 GAGAGA=0.116
East Asian Sub 86 GAGAGAGA=0.87 GAGAGA=0.13
Other Asian Sub 26 GAGAGAGA=0.92 GAGAGA=0.08
Latin American 1 Sub 146 GAGAGAGA=0.973 GAGAGA=0.027
Latin American 2 Sub 610 GAGAGAGA=0.925 GAGAGA=0.075
South Asian Sub 98 GAGAGAGA=0.96 GAGAGA=0.04
Other Sub 504 GAGAGAGA=0.974 GAGAGA=0.026


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
TopMed Global Study-wide 264690 (GA)4=0.979829 delGA=0.020171
gnomAD - Genomes Global Study-wide 140228 (GA)4=0.987442 delGA=0.012558
gnomAD - Genomes European Sub 75932 (GA)4=0.99921 delGA=0.00079
gnomAD - Genomes African Sub 42050 (GA)4=0.99013 delGA=0.00987
gnomAD - Genomes American Sub 13656 (GA)4=0.94310 delGA=0.05690
gnomAD - Genomes Ashkenazi Jewish Sub 3320 (GA)4=0.9922 delGA=0.0078
gnomAD - Genomes East Asian Sub 3118 (GA)4=0.8614 delGA=0.1386
gnomAD - Genomes Other Sub 2152 (GA)4=0.9763 delGA=0.0237
8.3KJPN JAPANESE Study-wide 16760 (GA)4=0.84553 delGA=0.15447
1000Genomes Global Study-wide 5008 (GA)4=0.9547 delGA=0.0453
1000Genomes African Sub 1322 (GA)4=0.9849 delGA=0.0151
1000Genomes East Asian Sub 1008 (GA)4=0.8730 delGA=0.1270
1000Genomes Europe Sub 1006 (GA)4=0.9990 delGA=0.0010
1000Genomes South Asian Sub 978 (GA)4=0.967 delGA=0.033
1000Genomes American Sub 694 (GA)4=0.934 delGA=0.066
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 (GA)4=0.9987 delGA=0.0013
UK 10K study - Twins TWIN COHORT Study-wide 3708 (GA)4=0.9995 delGA=0.0005
Korean Genome Project KOREAN Study-wide 1832 (GA)4=0.8483 delGA=0.1517
A Vietnamese Genetic Variation Database Global Study-wide 216 (GA)4=0.833 delGA=0.167

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 (GA)4= delGA
GRCh38.p13 chr 1 NC_000001.11:g.843931_843938= NC_000001.11:g.843931GA[3]
GRCh37.p13 chr 1 NC_000001.10:g.779311_779318= NC_000001.10:g.779311GA[3]

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#.

21 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 GMI ss154521623 Dec 01, 2009 (131)
2 GMI ss287939311 May 04, 2012 (137)
3 1000GENOMES ss325997456 May 09, 2011 (135)
4 1000GENOMES ss498763836 May 04, 2012 (137)
5 LUNTER ss552738996 Apr 25, 2013 (138)
6 TISHKOFF ss553708525 Apr 25, 2013 (138)
7 SSMP ss663205762 Apr 01, 2015 (144)
8 1000GENOMES ss1367645390 Aug 21, 2014 (142)
9 EVA_UK10K_ALSPAC ss1700142569 Apr 01, 2015 (144)
10 EVA_UK10K_TWINSUK ss1700153478 Apr 01, 2015 (144)
11 JJLAB ss2030297734 Sep 14, 2016 (149)
12 TOPMED ss2321504031 Dec 20, 2016 (150)
13 GNOMAD ss2750639639 Nov 08, 2017 (151)
14 SWEGEN ss2986149182 Nov 08, 2017 (151)
15 MCHAISSO ss3063573506 Nov 08, 2017 (151)
16 TOPMED ss3066401814 Nov 08, 2017 (151)
17 EVA_DECODE ss3685992232 Jul 12, 2019 (153)
18 KHV_HUMAN_GENOMES ss3798743688 Jul 12, 2019 (153)
19 KOGIC ss3943629766 Apr 25, 2020 (154)
20 TOPMED ss4436435225 Apr 25, 2021 (155)
21 TOMMO_GENOMICS ss5142052491 Apr 25, 2021 (155)
22 1000Genomes NC_000001.10 - 779311 Oct 11, 2018 (152)
23 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 779311 Oct 11, 2018 (152)
24 gnomAD - Genomes NC_000001.11 - 843931 Apr 25, 2021 (155)
25 Korean Genome Project NC_000001.11 - 843931 Apr 25, 2020 (154)
26 8.3KJPN NC_000001.10 - 779311 Apr 25, 2021 (155)
27 TopMed NC_000001.11 - 843931 Apr 25, 2021 (155)
28 UK 10K study - Twins NC_000001.10 - 779311 Oct 11, 2018 (152)
29 A Vietnamese Genetic Variation Database NC_000001.10 - 779311 Jul 12, 2019 (153)
30 ALFA NC_000001.11 - 843931 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).

Associated ID History Updated (Build)
rs147301185 Sep 17, 2011 (135)
rs371620064 May 15, 2013 (138)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss287939311, ss325997456, ss552738996 NC_000001.9:769173:GA: NC_000001.11:843930:GAGAGAGA:GAGAGA (self)
4359, 369, 21798, 369, 77, ss498763836, ss663205762, ss1367645390, ss1700142569, ss1700153478, ss2030297734, ss2321504031, ss2750639639, ss2986149182, ss5142052491 NC_000001.10:779310:GA: NC_000001.11:843930:GAGAGAGA:GAGAGA (self)
ss553708525 NC_000001.10:779316:GA: NC_000001.11:843930:GAGAGAGA:GAGAGA (self)
67146, 7767, 18309, 41560, ss3063573506, ss3066401814, ss3685992232, ss3798743688, ss3943629766, ss4436435225 NC_000001.11:843930:GA: NC_000001.11:843930:GAGAGAGA:GAGAGA (self)
5497015840 NC_000001.11:843930:GAGAGAGA:GAGAGA NC_000001.11:843930:GAGAGAGA:GAGAGA (self)
ss154521623 NT_004350.19:257942:GA: NC_000001.11:843930:GAGAGAGA:GAGAGA (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 rs80302052


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