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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.

rs16858623

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:167170449 (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.

Alleles
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.038022 (10064/264690, TOPMED)
G=0.035983 (5046/140234, GnomAD)
G=0.05574 (4387/78700, PAGE_STUDY) (+ 9 more)
G=0.01642 (425/25890, ALFA)
G=0.0347 (174/5008, 1000G)
G=0.0008 (3/3854, ALSPAC)
G=0.0003 (1/3708, TWINSUK)
G=0.077 (77/998, HapMap)
G=0.002 (1/626, Chileans)
G=0.042 (9/216, Qatari)
A=0.50 (12/24, SGDP_PRJ)
G=0.50 (12/24, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC105371601 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr 1 NC_000001.11:g.167170449A>G
GRCh37.p13 chr 1 NC_000001.10:g.167139686A>G
Gene: LOC105371601, uncharacterized LOC105371601 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105371601 transcript XR_922250.2: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

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 25890 A=0.98358 G=0.01642
European Sub 20312 A=0.99975 G=0.00025
African Sub 3174 A=0.8800 G=0.1200
African Others Sub 124 A=0.855 G=0.145
African American Sub 3050 A=0.8810 G=0.1190
Asian Sub 162 A=1.000 G=0.000
East Asian Sub 134 A=1.000 G=0.000
Other Asian Sub 28 A=1.00 G=0.00
Latin American 1 Sub 168 A=0.976 G=0.024
Latin American 2 Sub 700 A=0.993 G=0.007
South Asian Sub 120 A=1.000 G=0.000
Other Sub 1254 A=0.9761 G=0.0239


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=0.961978 G=0.038022
gnomAD - Genomes Global Study-wide 140234 A=0.964017 G=0.035983
gnomAD - Genomes European Sub 75954 A=0.99971 G=0.00029
gnomAD - Genomes African Sub 42016 A=0.88730 G=0.11270
gnomAD - Genomes American Sub 13662 A=0.98375 G=0.01625
gnomAD - Genomes Ashkenazi Jewish Sub 3318 A=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3132 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2152 A=0.9689 G=0.0311
The PAGE Study Global Study-wide 78700 A=0.94426 G=0.05574
The PAGE Study AfricanAmerican Sub 32516 A=0.89073 G=0.10927
The PAGE Study Mexican Sub 10810 A=0.99500 G=0.00500
The PAGE Study Asian Sub 8316 A=0.9999 G=0.0001
The PAGE Study PuertoRican Sub 7918 A=0.9529 G=0.0471
The PAGE Study NativeHawaiian Sub 4534 A=0.9980 G=0.0020
The PAGE Study Cuban Sub 4230 A=0.9816 G=0.0184
The PAGE Study Dominican Sub 3828 A=0.9423 G=0.0577
The PAGE Study CentralAmerican Sub 2450 A=0.9763 G=0.0237
The PAGE Study SouthAmerican Sub 1982 A=0.9914 G=0.0086
The PAGE Study NativeAmerican Sub 1260 A=0.9817 G=0.0183
The PAGE Study SouthAsian Sub 856 A=1.000 G=0.000
Allele Frequency Aggregator Total Global 25890 A=0.98358 G=0.01642
Allele Frequency Aggregator European Sub 20312 A=0.99975 G=0.00025
Allele Frequency Aggregator African Sub 3174 A=0.8800 G=0.1200
Allele Frequency Aggregator Other Sub 1254 A=0.9761 G=0.0239
Allele Frequency Aggregator Latin American 2 Sub 700 A=0.993 G=0.007
Allele Frequency Aggregator Latin American 1 Sub 168 A=0.976 G=0.024
Allele Frequency Aggregator Asian Sub 162 A=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 120 A=1.000 G=0.000
1000Genomes Global Study-wide 5008 A=0.9653 G=0.0347
1000Genomes African Sub 1322 A=0.8759 G=0.1241
1000Genomes East Asian Sub 1008 A=1.0000 G=0.0000
1000Genomes Europe Sub 1006 A=0.9990 G=0.0010
1000Genomes South Asian Sub 978 A=1.000 G=0.000
1000Genomes American Sub 694 A=0.987 G=0.013
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9992 G=0.0008
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9997 G=0.0003
HapMap Global Study-wide 998 A=0.923 G=0.077
HapMap African Sub 692 A=0.909 G=0.091
HapMap American Sub 216 A=0.935 G=0.065
HapMap Asian Sub 90 A=1.00 G=0.00
Chileans Chilean Study-wide 626 A=0.998 G=0.002
Qatari Global Study-wide 216 A=0.958 G=0.042
SGDP_PRJ Global Study-wide 24 A=0.50 G=0.50
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.p13 chr 1 NC_000001.11:g.167170449= NC_000001.11:g.167170449A>G
GRCh37.p13 chr 1 NC_000001.10:g.167139686= NC_000001.10:g.167139686A>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#.

36 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss23145066 Sep 20, 2004 (123)
2 KRIBB_YJKIM ss83070451 Dec 14, 2007 (130)
3 HGSV ss85942836 Dec 15, 2007 (130)
4 1000GENOMES ss210661855 Jul 14, 2010 (132)
5 1000GENOMES ss218698173 Jul 14, 2010 (132)
6 ILLUMINA ss480838801 May 04, 2012 (137)
7 ILLUMINA ss482132477 May 04, 2012 (137)
8 ILLUMINA ss533975418 Sep 08, 2015 (146)
9 TISHKOFF ss554807990 Apr 25, 2013 (138)
10 ILLUMINA ss779797752 Aug 21, 2014 (142)
11 ILLUMINA ss781330987 Aug 21, 2014 (142)
12 ILLUMINA ss835273717 Aug 21, 2014 (142)
13 JMKIDD_LAB ss1068337154 Aug 21, 2014 (142)
14 1000GENOMES ss1293281358 Aug 21, 2014 (142)
15 EVA_UK10K_ALSPAC ss1601403196 Apr 01, 2015 (144)
16 EVA_UK10K_TWINSUK ss1644397229 Apr 01, 2015 (144)
17 HAMMER_LAB ss1795217938 Sep 08, 2015 (146)
18 WEILL_CORNELL_DGM ss1919012599 Feb 12, 2016 (147)
19 ILLUMINA ss1958328847 Feb 12, 2016 (147)
20 JJLAB ss2020021879 Sep 14, 2016 (149)
21 HUMAN_LONGEVITY ss2167250908 Dec 20, 2016 (150)
22 TOPMED ss2329787013 Dec 20, 2016 (150)
23 ILLUMINA ss2632588213 Nov 08, 2017 (151)
24 GNOMAD ss2762317540 Nov 08, 2017 (151)
25 ILLUMINA ss3021147918 Nov 08, 2017 (151)
26 TOPMED ss3094436548 Nov 08, 2017 (151)
27 ILLUMINA ss3626231760 Oct 11, 2018 (152)
28 ILLUMINA ss3630620321 Oct 11, 2018 (152)
29 ILLUMINA ss3641621748 Oct 11, 2018 (152)
30 ILLUMINA ss3651484498 Oct 11, 2018 (152)
31 EVA_DECODE ss3687956515 Jul 12, 2019 (153)
32 ILLUMINA ss3725076286 Jul 12, 2019 (153)
33 PAGE_CC ss3770849467 Jul 12, 2019 (153)
34 KHV_HUMAN_GENOMES ss3799918346 Jul 12, 2019 (153)
35 SGDP_PRJ ss3850189709 Apr 25, 2020 (154)
36 TOPMED ss4471401863 Apr 25, 2021 (155)
37 1000Genomes NC_000001.10 - 167139686 Oct 11, 2018 (152)
38 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 167139686 Oct 11, 2018 (152)
39 Chileans NC_000001.10 - 167139686 Apr 25, 2020 (154)
40 gnomAD - Genomes NC_000001.11 - 167170449 Apr 25, 2021 (155)
41 HapMap NC_000001.11 - 167170449 Apr 25, 2020 (154)
42 The PAGE Study NC_000001.11 - 167170449 Jul 12, 2019 (153)
43 Qatari NC_000001.10 - 167139686 Apr 25, 2020 (154)
44 SGDP_PRJ NC_000001.10 - 167139686 Apr 25, 2020 (154)
45 TopMed NC_000001.11 - 167170449 Apr 25, 2021 (155)
46 UK 10K study - Twins NC_000001.10 - 167139686 Oct 11, 2018 (152)
47 ALFA NC_000001.11 - 167170449 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).

Associated ID History Updated (Build)
rs57042079 Feb 27, 2009 (130)
rs59881946 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss85942836 NC_000001.8:163871343:A:G NC_000001.11:167170448:A:G (self)
ss210661855, ss482132477 NC_000001.9:165406309:A:G NC_000001.11:167170448:A:G (self)
4085275, 2228441, 23585, 1054529, 2206689, 2228441, ss218698173, ss480838801, ss533975418, ss554807990, ss779797752, ss781330987, ss835273717, ss1068337154, ss1293281358, ss1601403196, ss1644397229, ss1795217938, ss1919012599, ss1958328847, ss2020021879, ss2329787013, ss2632588213, ss2762317540, ss3021147918, ss3626231760, ss3630620321, ss3641621748, ss3651484498, ss3850189709 NC_000001.10:167139685:A:G NC_000001.11:167170448:A:G (self)
29597290, 196153, 70936, 21973620, 35008198, 1074048213, ss2167250908, ss3094436548, ss3687956515, ss3725076286, ss3770849467, ss3799918346, ss4471401863 NC_000001.11:167170448:A:G NC_000001.11:167170448:A:G (self)
ss23145066, ss83070451 NT_004487.19:18628327:A:G NC_000001.11:167170448: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 rs16858623

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.post596+ae089ad