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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.

rs16854592

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:231587679 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.029351 (7769/264690, TOPMED)
G=0.022963 (3220/140224, GnomAD)
G=0.26504 (7489/28256, 14KJPN) (+ 18 more)
G=0.01796 (389/21654, ALFA)
G=0.27070 (4537/16760, 8.3KJPN)
G=0.0868 (556/6404, 1000G_30x)
G=0.0919 (460/5008, 1000G)
G=0.0114 (51/4480, Estonian)
G=0.0112 (43/3854, ALSPAC)
G=0.0051 (19/3708, TWINSUK)
G=0.2539 (744/2930, KOREAN)
G=0.2429 (445/1832, Korea1K)
G=0.0975 (174/1784, HapMap)
G=0.004 (4/998, GoNL)
G=0.007 (4/600, NorthernSweden)
G=0.037 (8/216, Qatari)
G=0.202 (42/208, Vietnamese)
A=0.424 (50/118, SGDP_PRJ)
G=0.03 (1/40, GENOME_DK)
A=0.50 (8/16, Siberian)
G=0.50 (8/16, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TSNAX-DISC1 : 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 21654 A=0.98204 G=0.01796
European Sub 15666 A=0.98953 G=0.01047
African Sub 3622 A=0.9663 G=0.0337
African Others Sub 126 A=0.960 G=0.040
African American Sub 3496 A=0.9665 G=0.0335
Asian Sub 160 A=0.731 G=0.269
East Asian Sub 102 A=0.716 G=0.284
Other Asian Sub 58 A=0.76 G=0.24
Latin American 1 Sub 212 A=0.995 G=0.005
Latin American 2 Sub 754 A=0.975 G=0.025
South Asian Sub 110 A=0.927 G=0.073
Other Sub 1130 A=0.9717 G=0.0283


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 A=0.970649 G=0.029351
gnomAD - Genomes Global Study-wide 140224 A=0.977037 G=0.022963
gnomAD - Genomes European Sub 75946 A=0.99006 G=0.00994
gnomAD - Genomes African Sub 42022 A=0.96892 G=0.03108
gnomAD - Genomes American Sub 13654 A=0.98140 G=0.01860
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.9847 G=0.0153
gnomAD - Genomes East Asian Sub 3126 A=0.7482 G=0.2518
gnomAD - Genomes Other Sub 2152 A=0.9689 G=0.0311
14KJPN JAPANESE Study-wide 28256 A=0.73496 G=0.26504
Allele Frequency Aggregator Total Global 21654 A=0.98204 G=0.01796
Allele Frequency Aggregator European Sub 15666 A=0.98953 G=0.01047
Allele Frequency Aggregator African Sub 3622 A=0.9663 G=0.0337
Allele Frequency Aggregator Other Sub 1130 A=0.9717 G=0.0283
Allele Frequency Aggregator Latin American 2 Sub 754 A=0.975 G=0.025
Allele Frequency Aggregator Latin American 1 Sub 212 A=0.995 G=0.005
Allele Frequency Aggregator Asian Sub 160 A=0.731 G=0.269
Allele Frequency Aggregator South Asian Sub 110 A=0.927 G=0.073
8.3KJPN JAPANESE Study-wide 16760 A=0.72930 G=0.27070
1000Genomes_30x Global Study-wide 6404 A=0.9132 G=0.0868
1000Genomes_30x African Sub 1786 A=0.9714 G=0.0286
1000Genomes_30x Europe Sub 1266 A=0.9882 G=0.0118
1000Genomes_30x South Asian Sub 1202 A=0.8785 G=0.1215
1000Genomes_30x East Asian Sub 1170 A=0.7248 G=0.2752
1000Genomes_30x American Sub 980 A=0.978 G=0.022
1000Genomes Global Study-wide 5008 A=0.9081 G=0.0919
1000Genomes African Sub 1322 A=0.9697 G=0.0303
1000Genomes East Asian Sub 1008 A=0.7252 G=0.2748
1000Genomes Europe Sub 1006 A=0.9881 G=0.0119
1000Genomes South Asian Sub 978 A=0.880 G=0.120
1000Genomes American Sub 694 A=0.980 G=0.020
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.9886 G=0.0114
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9888 G=0.0112
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9949 G=0.0051
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.7461 G=0.2539
Korean Genome Project KOREAN Study-wide 1832 A=0.7571 G=0.2429
HapMap Global Study-wide 1784 A=0.9025 G=0.0975
HapMap African Sub 692 A=0.965 G=0.035
HapMap American Sub 662 A=0.899 G=0.101
HapMap Asian Sub 254 A=0.677 G=0.323
HapMap Europe Sub 176 A=0.994 G=0.006
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.996 G=0.004
Northern Sweden ACPOP Study-wide 600 A=0.993 G=0.007
Qatari Global Study-wide 216 A=0.963 G=0.037
A Vietnamese Genetic Variation Database Global Study-wide 208 A=0.798 G=0.202
SGDP_PRJ Global Study-wide 118 A=0.424 G=0.576
The Danish reference pan genome Danish Study-wide 40 A=0.97 G=0.03
Siberian Global Study-wide 16 A=0.50 G=0.50
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 1 NC_000001.11:g.231587679A>G
GRCh37.p13 chr 1 NC_000001.10:g.231723425A>G
Gene: TSNAX-DISC1, TSNAX-DISC1 readthrough (NMD candidate) (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TSNAX-DISC1 transcript variant 1 NR_028393.1:n. N/A Intron Variant
TSNAX-DISC1 transcript variant 2 NR_028394.1:n. N/A Intron Variant
TSNAX-DISC1 transcript variant 3 NR_028395.1:n. N/A Intron Variant
TSNAX-DISC1 transcript variant 4 NR_028396.1:n. N/A Intron Variant
TSNAX-DISC1 transcript variant 5 NR_028397.1:n. N/A Intron Variant
TSNAX-DISC1 transcript variant 6 NR_028398.1:n. N/A Intron Variant
TSNAX-DISC1 transcript variant 7 NR_028399.1:n. N/A Intron Variant
TSNAX-DISC1 transcript variant 8 NR_028400.1:n. N/A Intron 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 A= G
GRCh38.p14 chr 1 NC_000001.11:g.231587679= NC_000001.11:g.231587679A>G
GRCh37.p13 chr 1 NC_000001.10:g.231723425= NC_000001.10:g.231723425A>G
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#.

50 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss23887960 Sep 20, 2004 (123)
2 AFFY ss76627942 Dec 07, 2007 (129)
3 KRIBB_YJKIM ss105079872 Feb 04, 2009 (130)
4 1000GENOMES ss210763312 Jul 14, 2010 (132)
5 1000GENOMES ss218937147 Jul 14, 2010 (132)
6 1000GENOMES ss230943567 Jul 14, 2010 (132)
7 1000GENOMES ss238549680 Jul 15, 2010 (132)
8 GMI ss276258528 May 04, 2012 (137)
9 CSHL ss472328951 May 04, 2012 (137)
10 TISHKOFF ss555204417 Apr 25, 2013 (138)
11 SSMP ss648777335 Apr 25, 2013 (138)
12 EVA-GONL ss976253086 Aug 21, 2014 (142)
13 JMKIDD_LAB ss1068683674 Aug 21, 2014 (142)
14 1000GENOMES ss1295060089 Aug 21, 2014 (142)
15 EVA_GENOME_DK ss1574746993 Apr 01, 2015 (144)
16 EVA_DECODE ss1585652771 Apr 01, 2015 (144)
17 EVA_UK10K_ALSPAC ss1602358150 Apr 01, 2015 (144)
18 EVA_UK10K_TWINSUK ss1645352183 Apr 01, 2015 (144)
19 EVA_SVP ss1712413398 Apr 01, 2015 (144)
20 WEILL_CORNELL_DGM ss1919474330 Feb 12, 2016 (147)
21 GENOMED ss1966998375 Jul 19, 2016 (147)
22 CSHL ss2136844944 Nov 08, 2017 (151)
23 USC_VALOUEV ss2148298543 Dec 20, 2016 (150)
24 HUMAN_LONGEVITY ss2170931924 Dec 20, 2016 (150)
25 SYSTEMSBIOZJU ss2624643298 Nov 08, 2017 (151)
26 GRF ss2698298633 Nov 08, 2017 (151)
27 GNOMAD ss2767380795 Nov 08, 2017 (151)
28 SWEGEN ss2988619428 Nov 08, 2017 (151)
29 EGCUT_WGS ss3656578174 Jul 12, 2019 (153)
30 EVA_DECODE ss3688831627 Jul 12, 2019 (153)
31 ACPOP ss3727951650 Jul 12, 2019 (153)
32 EVA ss3747465553 Jul 12, 2019 (153)
33 KHV_HUMAN_GENOMES ss3800467494 Jul 12, 2019 (153)
34 SGDP_PRJ ss3851111557 Apr 25, 2020 (154)
35 KRGDB ss3896459295 Apr 25, 2020 (154)
36 KOGIC ss3946706542 Apr 25, 2020 (154)
37 TOPMED ss4487172998 Apr 25, 2021 (155)
38 TOMMO_GENOMICS ss5148903921 Apr 25, 2021 (155)
39 1000G_HIGH_COVERAGE ss5246153915 Oct 13, 2022 (156)
40 EVA ss5325444606 Oct 13, 2022 (156)
41 HUGCELL_USP ss5446554166 Oct 13, 2022 (156)
42 EVA ss5506226589 Oct 13, 2022 (156)
43 1000G_HIGH_COVERAGE ss5520431176 Oct 13, 2022 (156)
44 SANFORD_IMAGENETICS ss5627649960 Oct 13, 2022 (156)
45 TOMMO_GENOMICS ss5676801391 Oct 13, 2022 (156)
46 YY_MCH ss5801730562 Oct 13, 2022 (156)
47 EVA ss5833407312 Oct 13, 2022 (156)
48 EVA ss5849331158 Oct 13, 2022 (156)
49 EVA ss5912386458 Oct 13, 2022 (156)
50 EVA ss5939498205 Oct 13, 2022 (156)
51 1000Genomes NC_000001.10 - 231723425 Oct 11, 2018 (152)
52 1000Genomes_30x NC_000001.11 - 231587679 Oct 13, 2022 (156)
53 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 231723425 Oct 11, 2018 (152)
54 Genetic variation in the Estonian population NC_000001.10 - 231723425 Oct 11, 2018 (152)
55 The Danish reference pan genome NC_000001.10 - 231723425 Apr 25, 2020 (154)
56 gnomAD - Genomes NC_000001.11 - 231587679 Apr 25, 2021 (155)
57 Genome of the Netherlands Release 5 NC_000001.10 - 231723425 Apr 25, 2020 (154)
58 HapMap NC_000001.11 - 231587679 Apr 25, 2020 (154)
59 KOREAN population from KRGDB NC_000001.10 - 231723425 Apr 25, 2020 (154)
60 Korean Genome Project NC_000001.11 - 231587679 Apr 25, 2020 (154)
61 Northern Sweden NC_000001.10 - 231723425 Jul 12, 2019 (153)
62 Qatari NC_000001.10 - 231723425 Apr 25, 2020 (154)
63 SGDP_PRJ NC_000001.10 - 231723425 Apr 25, 2020 (154)
64 Siberian NC_000001.10 - 231723425 Apr 25, 2020 (154)
65 8.3KJPN NC_000001.10 - 231723425 Apr 25, 2021 (155)
66 14KJPN NC_000001.11 - 231587679 Oct 13, 2022 (156)
67 TopMed NC_000001.11 - 231587679 Apr 25, 2021 (155)
68 UK 10K study - Twins NC_000001.10 - 231723425 Oct 11, 2018 (152)
69 A Vietnamese Genetic Variation Database NC_000001.10 - 231723425 Jul 12, 2019 (153)
70 ALFA NC_000001.11 - 231587679 Apr 25, 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
ss210763312, ss276258528, ss1585652771, ss1712413398, ss2136844944 NC_000001.9:229790047:A:G NC_000001.11:231587678:A:G (self)
5929511, 3278871, 2316422, 1927934, 1433253, 3636689, 1236515, 1516260, 3128537, 814897, 6873228, 3278871, 713217, ss218937147, ss230943567, ss238549680, ss555204417, ss648777335, ss976253086, ss1068683674, ss1295060089, ss1574746993, ss1602358150, ss1645352183, ss1919474330, ss1966998375, ss2148298543, ss2624643298, ss2698298633, ss2767380795, ss2988619428, ss3656578174, ss3727951650, ss3747465553, ss3851111557, ss3896459295, ss5148903921, ss5325444606, ss5506226589, ss5627649960, ss5833407312, ss5939498205 NC_000001.10:231723424:A:G NC_000001.11:231587678:A:G (self)
7957111, 42539297, 289243, 3084543, 10638495, 50779333, 10104573759, ss2170931924, ss3688831627, ss3800467494, ss3946706542, ss4487172998, ss5246153915, ss5446554166, ss5520431176, ss5676801391, ss5801730562, ss5849331158, ss5912386458 NC_000001.11:231587678:A:G NC_000001.11:231587678:A:G (self)
ss23887960, ss76627942, ss105079872, ss472328951 NT_167186.1:25241203:A:G NC_000001.11:231587678:A:G (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 rs16854592

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