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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
chr1:274100-274103 (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
delAAGT=0.35817 (6003/16760, 8.3KJPN)
delAAGT=0.29924 (4886/16328, ALFA)
delAAGT=0.3428 (628/1832, Korea1K)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
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.274100_274103del
GRCh37.p13 chr 1 NC_000001.10:g.243851_243854del

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 16328 AAGT=0.70076 =0.29924
European Sub 12076 AAGT=0.65552 =0.34448
African Sub 2816 AAGT=0.8903 =0.1097
African Others Sub 108 AAGT=0.898 =0.102
African American Sub 2708 AAGT=0.8900 =0.1100
Asian Sub 108 AAGT=0.694 =0.306
East Asian Sub 84 AAGT=0.68 =0.32
Other Asian Sub 24 AAGT=0.75 =0.25
Latin American 1 Sub 146 AAGT=0.726 =0.274
Latin American 2 Sub 610 AAGT=0.682 =0.318
South Asian Sub 94 AAGT=0.65 =0.35
Other Sub 478 AAGT=0.755 =0.245


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
8.3KJPN JAPANESE Study-wide 16760 AAGT=0.64183 delAAGT=0.35817
Korean Genome Project KOREAN Study-wide 1832 AAGT=0.6572 delAAGT=0.3428

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 AAGT= delAAGT
GRCh38.p13 chr 1 NC_000001.11:g.274100_274103= NC_000001.11:g.274100_274103del
GRCh37.p13 chr 1 NC_000001.10:g.243851_243854= NC_000001.10:g.243851_243854del

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#.

15 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 GMI ss287939218 May 04, 2012 (137)
2 1000GENOMES ss325997437 May 09, 2011 (134)
3 LUNTER ss550903089 Apr 25, 2013 (138)
4 SSMP ss663174057 Apr 01, 2015 (144)
5 BILGI_BIOE ss666079962 Apr 25, 2013 (138)
6 GENOMED ss1966667291 Jul 19, 2016 (147)
7 GNOMAD ss2750615328 Nov 08, 2017 (151)
8 SWEGEN ss2986144235 Nov 08, 2017 (151)
9 TOPMED ss3066348991 Nov 08, 2017 (151)
10 URBANLAB ss3646580795 Oct 11, 2018 (152)
11 EVA_DECODE ss3685991054 Jul 12, 2019 (153)
12 PACBIO ss3788979665 Jul 12, 2019 (153)
13 PACBIO ss3793852245 Jul 12, 2019 (153)
14 KOGIC ss3943625000 Apr 25, 2020 (154)
15 TOMMO_GENOMICS ss5142039808 Apr 25, 2021 (155)
16 Korean Genome Project NC_000001.11 - 274100 Apr 25, 2020 (154)
17 8.3KJPN NC_000001.10 - 243851 Apr 25, 2021 (155)
18 ALFA NC_000001.11 - 274100 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
ss287939218, ss325997437, ss550903089 NC_000001.9:233713:AAGT: NC_000001.11:274099:AAGT: (self)
9115, ss663174057, ss666079962, ss1966667291, ss2750615328, ss2986144235, ss3788979665, ss3793852245, ss5142039808 NC_000001.10:243850:AAGT: NC_000001.11:274099:AAGT: (self)
3001, 7073550943, ss3066348991, ss3646580795, ss3685991054, ss3943625000 NC_000001.11:274099:AAGT: NC_000001.11:274099:AAGT: (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 rs140116466


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