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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.

rs17109623

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:83045507 (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=0.123386 (32659/264690, TOPMED)
G=0.126847 (17770/140090, GnomAD)
G=0.09495 (2786/29342, ALFA) (+ 17 more)
G=0.00179 (30/16760, 8.3KJPN)
G=0.1282 (642/5008, 1000G)
G=0.1317 (590/4480, Estonian)
G=0.1495 (576/3854, ALSPAC)
G=0.1330 (493/3708, TWINSUK)
G=0.0034 (10/2922, KOREAN)
G=0.0066 (12/1832, Korea1K)
G=0.1150 (198/1722, HapMap)
G=0.166 (166/998, GoNL)
G=0.086 (54/626, Chileans)
G=0.103 (62/600, NorthernSweden)
G=0.167 (36/216, Qatari)
G=0.005 (1/214, Vietnamese)
A=0.421 (48/114, SGDP_PRJ)
G=0.12 (5/40, GENOME_DK)
A=0.5 (1/2, Siberian)
G=0.5 (1/2, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01362 : Intron Variant
LOC107985037 : 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.83045507A>G
GRCh37.p13 chr 1 NC_000001.10:g.83511190A>G
Gene: LINC01362, long intergenic non-protein coding RNA 1362 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01362 transcript NR_147074.1:n. N/A Intron Variant
Gene: LOC107985037, uncharacterized LOC107985037 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC107985037 transcript XR_001738121.1: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

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 29342 A=0.90505 G=0.09495
European Sub 21618 A=0.89342 G=0.10658
African Sub 3066 A=0.9426 G=0.0574
African Others Sub 112 A=0.938 G=0.062
African American Sub 2954 A=0.9428 G=0.0572
Asian Sub 160 A=1.000 G=0.000
East Asian Sub 102 A=1.000 G=0.000
Other Asian Sub 58 A=1.00 G=0.00
Latin American 1 Sub 264 A=0.932 G=0.068
Latin American 2 Sub 2686 A=0.9434 G=0.0566
South Asian Sub 58 A=0.97 G=0.03
Other Sub 1490 A=0.9101 G=0.0899


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=0.876614 G=0.123386
gnomAD - Genomes Global Study-wide 140090 A=0.873153 G=0.126847
gnomAD - Genomes European Sub 75888 A=0.86642 G=0.13358
gnomAD - Genomes African Sub 41976 A=0.87300 G=0.12700
gnomAD - Genomes American Sub 13626 A=0.88559 G=0.11441
gnomAD - Genomes Ashkenazi Jewish Sub 3322 A=0.8585 G=0.1415
gnomAD - Genomes East Asian Sub 3128 A=0.9965 G=0.0035
gnomAD - Genomes Other Sub 2150 A=0.8781 G=0.1219
Allele Frequency Aggregator Total Global 29342 A=0.90505 G=0.09495
Allele Frequency Aggregator European Sub 21618 A=0.89342 G=0.10658
Allele Frequency Aggregator African Sub 3066 A=0.9426 G=0.0574
Allele Frequency Aggregator Latin American 2 Sub 2686 A=0.9434 G=0.0566
Allele Frequency Aggregator Other Sub 1490 A=0.9101 G=0.0899
Allele Frequency Aggregator Latin American 1 Sub 264 A=0.932 G=0.068
Allele Frequency Aggregator Asian Sub 160 A=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 58 A=0.97 G=0.03
8.3KJPN JAPANESE Study-wide 16760 A=0.99821 G=0.00179
1000Genomes Global Study-wide 5008 A=0.8718 G=0.1282
1000Genomes African Sub 1322 A=0.8767 G=0.1233
1000Genomes East Asian Sub 1008 A=0.9990 G=0.0010
1000Genomes Europe Sub 1006 A=0.8658 G=0.1342
1000Genomes South Asian Sub 978 A=0.735 G=0.265
1000Genomes American Sub 694 A=0.879 G=0.121
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.8683 G=0.1317
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.8505 G=0.1495
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.8670 G=0.1330
KOREAN population from KRGDB KOREAN Study-wide 2922 A=0.9966 G=0.0034
Korean Genome Project KOREAN Study-wide 1832 A=0.9934 G=0.0066
HapMap Global Study-wide 1722 A=0.8850 G=0.1150
HapMap African Sub 692 A=0.890 G=0.110
HapMap American Sub 600 A=0.830 G=0.170
HapMap Asian Sub 254 A=0.996 G=0.004
HapMap Europe Sub 176 A=0.892 G=0.108
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.834 G=0.166
Chileans Chilean Study-wide 626 A=0.914 G=0.086
Northern Sweden ACPOP Study-wide 600 A=0.897 G=0.103
Qatari Global Study-wide 216 A=0.833 G=0.167
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.995 G=0.005
SGDP_PRJ Global Study-wide 114 A=0.421 G=0.579
The Danish reference pan genome Danish Study-wide 40 A=0.88 G=0.12
Siberian Global Study-wide 2 A=0.5 G=0.5
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.83045507= NC_000001.11:g.83045507A>G
GRCh37.p13 chr 1 NC_000001.10:g.83511190= NC_000001.10:g.83511190A>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#.

54 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss23145046 Sep 20, 2004 (123)
2 AFFY ss66410629 Dec 02, 2006 (127)
3 PERLEGEN ss68772215 May 18, 2007 (127)
4 AFFY ss76168248 Dec 07, 2007 (129)
5 KRIBB_YJKIM ss83195192 Dec 15, 2007 (130)
6 HUMANGENOME_JCVI ss99223094 Feb 03, 2009 (130)
7 1000GENOMES ss108366519 Jan 23, 2009 (130)
8 1000GENOMES ss110735377 Jan 25, 2009 (130)
9 ENSEMBL ss143265060 Dec 01, 2009 (131)
10 COMPLETE_GENOMICS ss163588461 Jul 04, 2010 (132)
11 AFFY ss172695584 Jul 20, 2010 (138)
12 BUSHMAN ss198701881 Jul 04, 2010 (132)
13 1000GENOMES ss218491736 Jul 14, 2010 (132)
14 1000GENOMES ss230612739 Jul 14, 2010 (132)
15 TISHKOFF ss554361964 Apr 25, 2013 (138)
16 SSMP ss648176080 Apr 25, 2013 (138)
17 EVA-GONL ss975365461 Aug 21, 2014 (142)
18 JMKIDD_LAB ss1068043517 Aug 21, 2014 (142)
19 1000GENOMES ss1291668463 Aug 21, 2014 (142)
20 EVA_GENOME_DK ss1574191691 Apr 01, 2015 (144)
21 EVA_DECODE ss1584739394 Apr 01, 2015 (144)
22 EVA_UK10K_ALSPAC ss1600582593 Apr 01, 2015 (144)
23 EVA_UK10K_TWINSUK ss1643576626 Apr 01, 2015 (144)
24 EVA_SVP ss1712348334 Apr 01, 2015 (144)
25 HAMMER_LAB ss1794651198 Sep 08, 2015 (146)
26 WEILL_CORNELL_DGM ss1918568440 Feb 12, 2016 (147)
27 GENOMED ss1966794056 Jul 19, 2016 (147)
28 JJLAB ss2019804870 Sep 14, 2016 (149)
29 USC_VALOUEV ss2147821958 Dec 20, 2016 (150)
30 HUMAN_LONGEVITY ss2164128792 Dec 20, 2016 (150)
31 TOPMED ss2326420988 Dec 20, 2016 (150)
32 GRF ss2697744131 Nov 08, 2017 (151)
33 GNOMAD ss2757360519 Nov 08, 2017 (151)
34 AFFY ss2984865692 Nov 08, 2017 (151)
35 AFFY ss2985518167 Nov 08, 2017 (151)
36 SWEGEN ss2987125277 Nov 08, 2017 (151)
37 BIOINF_KMB_FNS_UNIBA ss3023665216 Nov 08, 2017 (151)
38 TOPMED ss3081727468 Nov 08, 2017 (151)
39 CSHL ss3343543718 Nov 08, 2017 (151)
40 URBANLAB ss3646705705 Oct 11, 2018 (152)
41 ILLUMINA ss3653637270 Oct 11, 2018 (152)
42 EGCUT_WGS ss3655205772 Jul 12, 2019 (153)
43 EVA_DECODE ss3687150748 Jul 12, 2019 (153)
44 ACPOP ss3727216993 Jul 12, 2019 (153)
45 EVA ss3746440305 Jul 12, 2019 (153)
46 KHV_HUMAN_GENOMES ss3799446376 Jul 12, 2019 (153)
47 EVA ss3826271340 Apr 25, 2020 (154)
48 EVA ss3836524606 Apr 25, 2020 (154)
49 EVA ss3841931811 Apr 25, 2020 (154)
50 SGDP_PRJ ss3849250154 Apr 25, 2020 (154)
51 KRGDB ss3894301468 Apr 25, 2020 (154)
52 KOGIC ss3944881269 Apr 25, 2020 (154)
53 TOPMED ss4456684534 Apr 25, 2021 (155)
54 TOMMO_GENOMICS ss5144811235 Apr 25, 2021 (155)
55 1000Genomes NC_000001.10 - 83511190 Oct 11, 2018 (152)
56 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 83511190 Oct 11, 2018 (152)
57 Chileans NC_000001.10 - 83511190 Apr 25, 2020 (154)
58 Genetic variation in the Estonian population NC_000001.10 - 83511190 Oct 11, 2018 (152)
59 The Danish reference pan genome NC_000001.10 - 83511190 Apr 25, 2020 (154)
60 gnomAD - Genomes NC_000001.11 - 83045507 Apr 25, 2021 (155)
61 Genome of the Netherlands Release 5 NC_000001.10 - 83511190 Apr 25, 2020 (154)
62 HapMap NC_000001.11 - 83045507 Apr 25, 2020 (154)
63 KOREAN population from KRGDB NC_000001.10 - 83511190 Apr 25, 2020 (154)
64 Korean Genome Project NC_000001.11 - 83045507 Apr 25, 2020 (154)
65 Northern Sweden NC_000001.10 - 83511190 Jul 12, 2019 (153)
66 Qatari NC_000001.10 - 83511190 Apr 25, 2020 (154)
67 SGDP_PRJ NC_000001.10 - 83511190 Apr 25, 2020 (154)
68 Siberian NC_000001.10 - 83511190 Apr 25, 2020 (154)
69 8.3KJPN NC_000001.10 - 83511190 Apr 25, 2021 (155)
70 TopMed NC_000001.11 - 83045507 Apr 25, 2021 (155)
71 UK 10K study - Twins NC_000001.10 - 83511190 Oct 11, 2018 (152)
72 A Vietnamese Genetic Variation Database NC_000001.10 - 83511190 Jul 12, 2019 (153)
73 ALFA NC_000001.11 - 83045507 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)
rs61044389 Feb 26, 2009 (130)
rs118201496 Apr 25, 2013 (138)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss108366519, ss110735377, ss163588461, ss198701881, ss1584739394, ss1712348334 NC_000001.9:83283777:A:G NC_000001.11:83045506:A:G (self)
2415642, 1325843, 13818, 944020, 1583073, 572461, 1478862, 501858, 610370, 1267134, 338312, 2780542, 1325843, 284378, ss218491736, ss230612739, ss554361964, ss648176080, ss975365461, ss1068043517, ss1291668463, ss1574191691, ss1600582593, ss1643576626, ss1794651198, ss1918568440, ss1966794056, ss2019804870, ss2147821958, ss2326420988, ss2697744131, ss2757360519, ss2984865692, ss2985518167, ss2987125277, ss3343543718, ss3653637270, ss3655205772, ss3727216993, ss3746440305, ss3826271340, ss3836524606, ss3849250154, ss3894301468, ss5144811235 NC_000001.10:83511189:A:G NC_000001.11:83045506:A:G (self)
17048414, 112911, 1259270, 12780800, 20290869, 218800333, ss2164128792, ss3023665216, ss3081727468, ss3646705705, ss3687150748, ss3799446376, ss3841931811, ss3944881269, ss4456684534 NC_000001.11:83045506:A:G NC_000001.11:83045506:A:G (self)
ss23145046, ss66410629, ss68772215, ss76168248, ss83195192, ss99223094, ss143265060, ss172695584 NT_032977.9:53483107:A:G NC_000001.11:83045506: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 rs17109623

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