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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs140698854

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:163566841 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000094 (25/264690, TOPMED)
A=0.000208 (49/236016, GnomAD_exome)
A=0.000057 (8/140186, GnomAD) (+ 8 more)
A=0.000228 (24/105436, ExAC)
A=0.00184 (52/28258, 14KJPN)
A=0.00167 (28/16760, 8.3KJPN)
A=0.00014 (2/14420, ALFA)
A=0.0009 (6/6404, 1000G_30x)
A=0.0012 (6/5008, 1000G)
A=0.0024 (7/2922, KOREAN)
A=0.0016 (3/1832, Korea1K)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
QKI : 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 14420 G=0.99986 A=0.00014
European Sub 9824 G=1.0000 A=0.0000
African Sub 2946 G=1.0000 A=0.0000
African Others Sub 114 G=1.000 A=0.000
African American Sub 2832 G=1.0000 A=0.0000
Asian Sub 112 G=0.982 A=0.018
East Asian Sub 86 G=0.98 A=0.02
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 146 G=1.000 A=0.000
Latin American 2 Sub 610 G=1.000 A=0.000
South Asian Sub 98 G=1.00 A=0.00
Other Sub 684 G=1.000 A=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 G=0.999906 A=0.000094
gnomAD - Exomes Global Study-wide 236016 G=0.999792 A=0.000208
gnomAD - Exomes European Sub 126172 G=1.000000 A=0.000000
gnomAD - Exomes Asian Sub 46238 G=0.99898 A=0.00102
gnomAD - Exomes American Sub 32722 G=0.99997 A=0.00003
gnomAD - Exomes African Sub 15366 G=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 9680 G=1.0000 A=0.0000
gnomAD - Exomes Other Sub 5838 G=0.9998 A=0.0002
gnomAD - Genomes Global Study-wide 140186 G=0.999943 A=0.000057
gnomAD - Genomes European Sub 75912 G=1.00000 A=0.00000
gnomAD - Genomes African Sub 42028 G=0.99998 A=0.00002
gnomAD - Genomes American Sub 13656 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3124 G=0.9984 A=0.0016
gnomAD - Genomes Other Sub 2146 G=0.9991 A=0.0009
ExAC Global Study-wide 105436 G=0.999772 A=0.000228
ExAC Europe Sub 63476 G=1.00000 A=0.00000
ExAC Asian Sub 21994 G=0.99895 A=0.00105
ExAC American Sub 9814 G=0.9999 A=0.0001
ExAC African Sub 9344 G=1.0000 A=0.0000
ExAC Other Sub 808 G=1.000 A=0.000
14KJPN JAPANESE Study-wide 28258 G=0.99816 A=0.00184
8.3KJPN JAPANESE Study-wide 16760 G=0.99833 A=0.00167
Allele Frequency Aggregator Total Global 14420 G=0.99986 A=0.00014
Allele Frequency Aggregator European Sub 9824 G=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 2946 G=1.0000 A=0.0000
Allele Frequency Aggregator Other Sub 684 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 112 G=0.982 A=0.018
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00
1000Genomes_30x Global Study-wide 6404 G=0.9991 A=0.0009
1000Genomes_30x African Sub 1786 G=1.0000 A=0.0000
1000Genomes_30x Europe Sub 1266 G=1.0000 A=0.0000
1000Genomes_30x South Asian Sub 1202 G=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 G=0.9949 A=0.0051
1000Genomes_30x American Sub 980 G=1.000 A=0.000
1000Genomes Global Study-wide 5008 G=0.9988 A=0.0012
1000Genomes African Sub 1322 G=1.0000 A=0.0000
1000Genomes East Asian Sub 1008 G=0.9940 A=0.0060
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=1.000 A=0.000
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9976 A=0.0024
Korean Genome Project KOREAN Study-wide 1832 G=0.9984 A=0.0016
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 6 NC_000006.12:g.163566841G>A
GRCh37.p13 chr 6 NC_000006.11:g.163987873G>A
QKI RefSeqGene NG_029604.2:g.157199G>A
Gene: QKI, QKI, KH domain containing RNA binding (plus strand)
Molecule type Change Amino acid[Codon] SO Term
QKI transcript variant 5 NM_001301085.2:c.985+46G>A N/A Intron Variant
QKI transcript variant 1 NM_006775.3:c.1009+46G>A N/A Intron Variant
QKI transcript variant 4 NM_206855.3:c.*3096= N/A 3 Prime UTR Variant
QKI transcript variant 3 NM_206854.3:c.*2131= N/A 3 Prime UTR Variant
QKI transcript variant 2 NM_206853.3:c.*870= N/A 3 Prime UTR Variant
QKI transcript variant X2 XM_011536260.3:c.865+46G>A N/A Intron Variant
QKI transcript variant X1 XM_017011504.2:c.*870= N/A 3 Prime UTR Variant
QKI transcript variant X3 XM_047419566.1:c.*870= N/A 3 Prime UTR Variant
QKI transcript variant X4 XM_011536261.2:c. N/A Genic Downstream 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 G= A
GRCh38.p14 chr 6 NC_000006.12:g.163566841= NC_000006.12:g.163566841G>A
GRCh37.p13 chr 6 NC_000006.11:g.163987873= NC_000006.11:g.163987873G>A
QKI RefSeqGene NG_029604.2:g.157199= NG_029604.2:g.157199G>A
QKI transcript variant 4 NM_206855.3:c.*3096= NM_206855.3:c.*3096G>A
QKI transcript variant 4 NM_206855.2:c.*3096= NM_206855.2:c.*3096G>A
QKI transcript variant 3 NM_206854.3:c.*2131= NM_206854.3:c.*2131G>A
QKI transcript variant 3 NM_206854.2:c.*2131= NM_206854.2:c.*2131G>A
QKI transcript variant 2 NM_206853.3:c.*870= NM_206853.3:c.*870G>A
QKI transcript variant 2 NM_206853.2:c.*870= NM_206853.2:c.*870G>A
QKI transcript variant X1 XM_017011504.2:c.*870= XM_017011504.2:c.*870G>A
QKI transcript variant X9 XM_017011504.1:c.*870= XM_017011504.1:c.*870G>A
QKI transcript variant X3 XM_047419566.1:c.*870= XM_047419566.1:c.*870G>A
QKI transcript variant 5 NM_001301085.2:c.985+46= NM_001301085.2:c.985+46G>A
QKI transcript variant 1 NM_006775.2:c.1009+46= NM_006775.2:c.1009+46G>A
QKI transcript variant 1 NM_006775.3:c.1009+46= NM_006775.3:c.1009+46G>A
QKI transcript variant X1 XM_005267224.1:c.985+46= XM_005267224.1:c.985+46G>A
QKI transcript variant X3 XM_005267226.1:c.865+46= XM_005267226.1:c.865+46G>A
QKI transcript variant X2 XM_011536260.3:c.865+46= XM_011536260.3:c.865+46G>A
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#.

23 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss333797488 May 09, 2011 (134)
2 1000GENOMES ss490938653 May 04, 2012 (137)
3 SSMP ss654029621 Apr 25, 2013 (138)
4 1000GENOMES ss1323245567 Aug 21, 2014 (142)
5 EVA_EXAC ss1688581993 Apr 01, 2015 (144)
6 HUMAN_LONGEVITY ss2290401524 Dec 20, 2016 (150)
7 GNOMAD ss2736193316 Nov 08, 2017 (151)
8 GNOMAD ss2747743154 Nov 08, 2017 (151)
9 GNOMAD ss2847858949 Nov 08, 2017 (151)
10 EVA ss3765971342 Jul 13, 2019 (153)
11 KRGDB ss3913219774 Apr 26, 2020 (154)
12 KOGIC ss3960544211 Apr 26, 2020 (154)
13 TOPMED ss4730093476 Apr 26, 2021 (155)
14 TOMMO_GENOMICS ss5181019074 Apr 26, 2021 (155)
15 1000G_HIGH_COVERAGE ss5271206009 Oct 14, 2022 (156)
16 EVA ss5370566917 Oct 14, 2022 (156)
17 1000G_HIGH_COVERAGE ss5558569517 Oct 14, 2022 (156)
18 SANFORD_IMAGENETICS ss5641983726 Oct 14, 2022 (156)
19 TOMMO_GENOMICS ss5720216239 Oct 14, 2022 (156)
20 YY_MCH ss5808170173 Oct 14, 2022 (156)
21 EVA ss5886940715 Oct 14, 2022 (156)
22 EVA ss5971085918 Oct 14, 2022 (156)
23 EVA ss5971085919 Oct 14, 2022 (156)
24 1000Genomes NC_000006.11 - 163987873 Oct 12, 2018 (152)
25 1000Genomes_30x NC_000006.12 - 163566841 Oct 14, 2022 (156)
26 ExAC NC_000006.11 - 163987873 Oct 12, 2018 (152)
27 gnomAD - Genomes NC_000006.12 - 163566841 Apr 26, 2021 (155)
28 gnomAD - Exomes NC_000006.11 - 163987873 Jul 13, 2019 (153)
29 KOREAN population from KRGDB NC_000006.11 - 163987873 Apr 26, 2020 (154)
30 Korean Genome Project NC_000006.12 - 163566841 Apr 26, 2020 (154)
31 8.3KJPN NC_000006.11 - 163987873 Apr 26, 2021 (155)
32 14KJPN NC_000006.12 - 163566841 Oct 14, 2022 (156)
33 TopMed NC_000006.12 - 163566841 Apr 26, 2021 (155)
34 ALFA NC_000006.12 - 163566841 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
35151634, 8635832, 5349485, 20397168, 38988381, ss333797488, ss490938653, ss654029621, ss1323245567, ss1688581993, ss2736193316, ss2747743154, ss2847858949, ss3765971342, ss3913219774, ss5181019074, ss5370566917, ss5641983726, ss5971085918, ss5971085919 NC_000006.11:163987872:G:A NC_000006.12:163566840:G:A (self)
46095452, 248099242, 16922212, 54053343, 567471034, 13293464022, ss2290401524, ss3960544211, ss4730093476, ss5271206009, ss5558569517, ss5720216239, ss5808170173, ss5886940715 NC_000006.12:163566840:G:A NC_000006.12:163566840:G:A (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 rs140698854

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