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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
chr1:17398 (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.

C>A / C>T
Variation Type
SNV Single Nucleotide Variation
A=0.005788 (782/135096, GnomAD)
A=0.00354 (266/75238, GnomAD_exome)
A=0.00073 (13/17762, ALFA) (+ 4 more)
A=0.02142 (359/16758, 8.3KJPN)
A=0.0193 (105/5428, ExAC)
A=0.0140 (41/2922, KOREAN)
A=0.0344 (63/1832, Korea1K)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MIR6859-1 : Non Coding Transcript Variant
WASH7P : 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.17398C>A
GRCh38.p13 chr 1 NC_000001.11:g.17398C>T
GRCh37.p13 chr 1 NC_000001.10:g.17398C>A
GRCh37.p13 chr 1 NC_000001.10:g.17398C>T
Gene: MIR6859-1, microRNA 6859-1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
MIR6859-1 transcript NR_106918.1:n.39G>T N/A Non Coding Transcript Variant
MIR6859-1 transcript NR_106918.1:n.39G>A N/A Non Coding Transcript Variant
Gene: WASH7P, WASP family homolog 7, pseudogene (minus strand)
Molecule type Change Amino acid[Codon] SO Term
WASH7P transcript NR_024540.1:n. N/A Intron 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 17762 C=0.99927 A=0.00073, T=0.00000
European Sub 13150 C=0.99947 A=0.00053, T=0.00000
African Sub 2768 C=0.9996 A=0.0004, T=0.0000
African Others Sub 106 C=1.000 A=0.000, T=0.000
African American Sub 2662 C=0.9996 A=0.0004, T=0.0000
Asian Sub 132 C=1.000 A=0.000, T=0.000
East Asian Sub 96 C=1.00 A=0.00, T=0.00
Other Asian Sub 36 C=1.00 A=0.00, T=0.00
Latin American 1 Sub 142 C=1.000 A=0.000, T=0.000
Latin American 2 Sub 600 C=1.000 A=0.000, T=0.000
South Asian Sub 94 C=1.00 A=0.00, T=0.00
Other Sub 876 C=0.994 A=0.006, T=0.000


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 135096 C=0.994212 A=0.005788
gnomAD - Genomes European Sub 75084 C=0.99975 A=0.00025
gnomAD - Genomes African Sub 38684 C=0.98276 A=0.01724
gnomAD - Genomes American Sub 12984 C=0.99453 A=0.00547
gnomAD - Genomes Ashkenazi Jewish Sub 3270 C=0.9997 A=0.0003
gnomAD - Genomes East Asian Sub 3010 C=0.9973 A=0.0027
gnomAD - Genomes Other Sub 2064 C=0.9922 A=0.0078
gnomAD - Exomes Global Study-wide 75238 C=0.99646 A=0.00354
gnomAD - Exomes European Sub 41090 C=0.99944 A=0.00056
gnomAD - Exomes Asian Sub 14236 C=0.99600 A=0.00400
gnomAD - Exomes American Sub 10442 C=0.99416 A=0.00584
gnomAD - Exomes African Sub 5498 C=0.9796 A=0.0204
gnomAD - Exomes Other Sub 2184 C=0.9963 A=0.0037
gnomAD - Exomes Ashkenazi Jewish Sub 1788 C=0.9972 A=0.0028
8.3KJPN JAPANESE Study-wide 16758 C=0.97858 A=0.02142
ExAC Global Study-wide 5428 C=0.9807 A=0.0193
ExAC Europe Sub 3300 C=0.9945 A=0.0055
ExAC African Sub 980 C=0.929 A=0.071
ExAC Asian Sub 814 C=0.985 A=0.015
ExAC American Sub 278 C=0.982 A=0.018
ExAC Other Sub 56 C=1.00 A=0.00
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.9860 A=0.0140
Korean Genome Project KOREAN Study-wide 1832 C=0.9656 A=0.0344

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= A T
GRCh38.p13 chr 1 NC_000001.11:g.17398= NC_000001.11:g.17398C>A NC_000001.11:g.17398C>T
GRCh37.p13 chr 1 NC_000001.10:g.17398= NC_000001.10:g.17398C>A NC_000001.10:g.17398C>T
MIR6859-1 transcript NR_106918.1:n.39= NR_106918.1:n.39G>T NR_106918.1:n.39G>A

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#.

12 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 GMI ss275679869 May 04, 2012 (137)
2 CLINSEQ_SNP ss491581585 May 04, 2012 (137)
3 EVA_EXAC ss1685216856 Apr 01, 2015 (144)
4 GNOMAD ss2730985449 Nov 08, 2017 (151)
5 GNOMAD ss2746168695 Nov 08, 2017 (151)
6 GNOMAD ss2750601981 Nov 08, 2017 (151)
7 SWEGEN ss2986141480 Nov 08, 2017 (151)
8 TOPMED ss3066317567 Nov 08, 2017 (151)
9 KRGDB ss3892823080 Apr 25, 2020 (154)
10 KOGIC ss3943622215 Apr 25, 2020 (154)
11 TOMMO_GENOMICS ss5142031534 Apr 25, 2021 (155)
12 EVA ss5236862226 Apr 25, 2021 (155)
13 ExAC NC_000001.10 - 17398 Oct 11, 2018 (152)
14 gnomAD - Genomes NC_000001.11 - 17398 Apr 25, 2021 (155)
15 gnomAD - Exomes NC_000001.10 - 17398 Jul 12, 2019 (153)
16 KOREAN population from KRGDB NC_000001.10 - 17398 Apr 25, 2020 (154)
17 Korean Genome Project NC_000001.11 - 17398 Apr 25, 2020 (154)
18 8.3KJPN NC_000001.10 - 17398 Apr 25, 2021 (155)
19 ALFA NC_000001.11 - 17398 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
ss275679869, ss491581585 NC_000001.9:7260:C:A NC_000001.11:17397:C:A (self)
4389927, 61, 474, 841, ss1685216856, ss2730985449, ss2746168695, ss2750601981, ss2986141480, ss3892823080, ss5142031534 NC_000001.10:17397:C:A NC_000001.11:17397:C:A (self)
1671, 216, 4916978910, ss3066317567, ss3943622215, ss5236862226 NC_000001.11:17397:C:A NC_000001.11:17397:C:A (self)
ss2730985449 NC_000001.10:17397:C:T NC_000001.11:17397:C:T (self)
4916978910 NC_000001.11:17397:C:T NC_000001.11:17397:C:T

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

No publications for rs200784459


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