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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.

rs10789322

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:71713245 (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 / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.308761 (81726/264690, TOPMED)
A=0.303744 (42515/139970, GnomAD)
G=0.41712 (11787/28258, 14KJPN) (+ 17 more)
A=0.30616 (6602/21564, ALFA)
G=0.41814 (7008/16760, 8.3KJPN)
A=0.3097 (1983/6404, 1000G_30x)
A=0.3181 (1593/5008, 1000G)
A=0.4011 (1797/4480, Estonian)
A=0.3656 (1409/3854, ALSPAC)
A=0.3681 (1365/3708, TWINSUK)
G=0.4055 (1188/2930, KOREAN)
A=0.425 (424/998, GoNL)
G=0.439 (332/756, PRJEB37584)
A=0.287 (172/600, NorthernSweden)
A=0.304 (99/326, HapMap)
G=0.312 (100/320, SGDP_PRJ)
A=0.435 (94/216, Qatari)
G=0.463 (99/214, Vietnamese)
G=0.24 (10/42, Siberian)
A=0.42 (17/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NEGR1 : Intron Variant
Publications
1 citation
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 21564 G=0.69384 A=0.30616
European Sub 14286 G=0.62453 A=0.37547
African Sub 5568 G=0.9050 A=0.0950
African Others Sub 198 G=0.965 A=0.035
African American Sub 5370 G=0.9028 A=0.0972
Asian Sub 112 G=0.438 A=0.562
East Asian Sub 86 G=0.44 A=0.56
Other Asian Sub 26 G=0.42 A=0.58
Latin American 1 Sub 146 G=0.705 A=0.295
Latin American 2 Sub 610 G=0.464 A=0.536
South Asian Sub 98 G=0.74 A=0.26
Other Sub 744 G=0.663 A=0.337


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=0.691239 A=0.308761
gnomAD - Genomes Global Study-wide 139970 G=0.696256 A=0.303744
gnomAD - Genomes European Sub 75804 G=0.62158 A=0.37842
gnomAD - Genomes African Sub 41962 G=0.90053 A=0.09947
gnomAD - Genomes American Sub 13620 G=0.57269 A=0.42731
gnomAD - Genomes Ashkenazi Jewish Sub 3318 G=0.6049 A=0.3951
gnomAD - Genomes East Asian Sub 3124 G=0.4222 A=0.5778
gnomAD - Genomes Other Sub 2142 G=0.6643 A=0.3357
14KJPN JAPANESE Study-wide 28258 G=0.41712 A=0.58288
Allele Frequency Aggregator Total Global 21564 G=0.69384 A=0.30616
Allele Frequency Aggregator European Sub 14286 G=0.62453 A=0.37547
Allele Frequency Aggregator African Sub 5568 G=0.9050 A=0.0950
Allele Frequency Aggregator Other Sub 744 G=0.663 A=0.337
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.464 A=0.536
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.705 A=0.295
Allele Frequency Aggregator Asian Sub 112 G=0.438 A=0.562
Allele Frequency Aggregator South Asian Sub 98 G=0.74 A=0.26
8.3KJPN JAPANESE Study-wide 16760 G=0.41814 A=0.58186
1000Genomes_30x Global Study-wide 6404 G=0.6903 A=0.3097
1000Genomes_30x African Sub 1786 G=0.9580 A=0.0420
1000Genomes_30x Europe Sub 1266 G=0.6335 A=0.3665
1000Genomes_30x South Asian Sub 1202 G=0.7072 A=0.2928
1000Genomes_30x East Asian Sub 1170 G=0.4453 A=0.5547
1000Genomes_30x American Sub 980 G=0.548 A=0.452
1000Genomes Global Study-wide 5008 G=0.6819 A=0.3181
1000Genomes African Sub 1322 G=0.9531 A=0.0469
1000Genomes East Asian Sub 1008 G=0.4484 A=0.5516
1000Genomes Europe Sub 1006 G=0.6262 A=0.3738
1000Genomes South Asian Sub 978 G=0.706 A=0.294
1000Genomes American Sub 694 G=0.552 A=0.448
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.5989 A=0.4011
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.6344 A=0.3656
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.6319 A=0.3681
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.4055 A=0.5945, T=0.0000
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.575 A=0.425
CNV burdens in cranial meningiomas Global Study-wide 756 G=0.439 A=0.561
CNV burdens in cranial meningiomas CRM Sub 756 G=0.439 A=0.561
Northern Sweden ACPOP Study-wide 600 G=0.713 A=0.287
HapMap Global Study-wide 326 G=0.696 A=0.304
HapMap African Sub 120 G=0.975 A=0.025
HapMap American Sub 120 G=0.667 A=0.333
HapMap Asian Sub 86 G=0.35 A=0.65
SGDP_PRJ Global Study-wide 320 G=0.312 A=0.688
Qatari Global Study-wide 216 G=0.565 A=0.435
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.463 A=0.537
Siberian Global Study-wide 42 G=0.24 A=0.76
The Danish reference pan genome Danish Study-wide 40 G=0.57 A=0.42
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.71713245G>A
GRCh38.p14 chr 1 NC_000001.11:g.71713245G>T
GRCh37.p13 chr 1 NC_000001.10:g.72178928G>A
GRCh37.p13 chr 1 NC_000001.10:g.72178928G>T
Gene: NEGR1, neuronal growth regulator 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
NEGR1 transcript NM_173808.3:c.536-15106C>T N/A Intron Variant
NEGR1 transcript variant X1 XM_011541200.4:c.536-1510…

XM_011541200.4:c.536-15106C>T

 		N/A Intron Variant
NEGR1 transcript variant X2 XM_011541201.4:c.536-1510…

XM_011541201.4:c.536-15106C>T

 		N/A Intron Variant
NEGR1 transcript variant X3 XM_017000961.3:c.536-1510…

XM_017000961.3:c.536-15106C>T

 		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 G= A T
GRCh38.p14 chr 1 NC_000001.11:g.71713245= NC_000001.11:g.71713245G>A NC_000001.11:g.71713245G>T
GRCh37.p13 chr 1 NC_000001.10:g.72178928= NC_000001.10:g.72178928G>A NC_000001.10:g.72178928G>T
NEGR1 transcript NM_173808.2:c.536-15106= NM_173808.2:c.536-15106C>T NM_173808.2:c.536-15106C>A
NEGR1 transcript NM_173808.3:c.536-15106= NM_173808.3:c.536-15106C>T NM_173808.3:c.536-15106C>A
NEGR1 transcript variant X1 XM_005270723.1:c.535+62927= XM_005270723.1:c.535+62927C>T XM_005270723.1:c.535+62927C>A
NEGR1 transcript variant X1 XM_011541200.4:c.536-15106= XM_011541200.4:c.536-15106C>T XM_011541200.4:c.536-15106C>A
NEGR1 transcript variant X2 XM_011541201.4:c.536-15106= XM_011541201.4:c.536-15106C>T XM_011541201.4:c.536-15106C>A
NEGR1 transcript variant X3 XM_017000961.3:c.536-15106= XM_017000961.3:c.536-15106C>T XM_017000961.3:c.536-15106C>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#.

71 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss15430512 Feb 27, 2004 (120)
2 SC_SNP ss18199106 Feb 27, 2004 (120)
3 SC_SNP ss18288070 Feb 27, 2004 (120)
4 CSHL-HAPMAP ss19143414 Feb 27, 2004 (120)
5 SSAHASNP ss20474026 Apr 05, 2004 (121)
6 ABI ss41061898 Mar 15, 2006 (126)
7 BCMHGSC_JDW ss87530257 Mar 23, 2008 (129)
8 HUMANGENOME_JCVI ss97946719 Feb 05, 2009 (130)
9 BGI ss106575253 Feb 05, 2009 (130)
10 ENSEMBL ss137996779 Dec 01, 2009 (131)
11 ENSEMBL ss138904684 Dec 01, 2009 (131)
12 GMI ss155161028 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss164526058 Jul 04, 2010 (132)
14 BUSHMAN ss198604740 Jul 04, 2010 (132)
15 BCM-HGSC-SUB ss205203703 Jul 04, 2010 (132)
16 1000GENOMES ss218448245 Jul 14, 2010 (132)
17 1000GENOMES ss230580793 Jul 14, 2010 (132)
18 1000GENOMES ss238265955 Jul 15, 2010 (132)
19 GMI ss275871596 May 04, 2012 (137)
20 GMI ss284070762 Apr 25, 2013 (138)
21 PJP ss290534716 May 09, 2011 (134)
22 SSMP ss648120785 Apr 25, 2013 (138)
23 EVA-GONL ss975280009 Aug 21, 2014 (142)
24 JMKIDD_LAB ss1067979017 Aug 21, 2014 (142)
25 1000GENOMES ss1291351435 Aug 21, 2014 (142)
26 DDI ss1425848230 Apr 01, 2015 (144)
27 EVA_GENOME_DK ss1574139515 Apr 01, 2015 (144)
28 EVA_DECODE ss1584651472 Apr 01, 2015 (144)
29 EVA_UK10K_ALSPAC ss1600418188 Apr 01, 2015 (144)
30 EVA_UK10K_TWINSUK ss1643412221 Apr 01, 2015 (144)
31 WEILL_CORNELL_DGM ss1918486810 Feb 12, 2016 (147)
32 GENOMED ss1966774301 Jul 19, 2016 (147)
33 JJLAB ss2019761125 Sep 14, 2016 (149)
34 USC_VALOUEV ss2147777538 Dec 20, 2016 (150)
35 HUMAN_LONGEVITY ss2163465900 Dec 20, 2016 (150)
36 SYSTEMSBIOZJU ss2624393736 Nov 08, 2017 (151)
37 ILLUMINA ss2632530811 Nov 08, 2017 (151)
38 GRF ss2697696993 Nov 08, 2017 (151)
39 GNOMAD ss2756454255 Nov 08, 2017 (151)
40 SWEGEN ss2986999398 Nov 08, 2017 (151)
41 BIOINF_KMB_FNS_UNIBA ss3023642595 Nov 08, 2017 (151)
42 CSHL ss3343507078 Nov 08, 2017 (151)
43 URBANLAB ss3646687811 Oct 11, 2018 (152)
44 EGCUT_WGS ss3655072713 Jul 12, 2019 (153)
45 EVA_DECODE ss3686996488 Jul 12, 2019 (153)
46 ACPOP ss3727147135 Jul 12, 2019 (153)
47 EVA ss3746344943 Jul 12, 2019 (153)
48 PACBIO ss3783441912 Jul 12, 2019 (153)
49 PACBIO ss3789095171 Jul 12, 2019 (153)
50 PACBIO ss3793967918 Jul 12, 2019 (153)
51 KHV_HUMAN_GENOMES ss3799350925 Jul 12, 2019 (153)
52 EVA ss3826230794 Apr 25, 2020 (154)
53 EVA ss3836503263 Apr 25, 2020 (154)
54 EVA ss3841909985 Apr 25, 2020 (154)
55 SGDP_PRJ ss3849085634 Apr 25, 2020 (154)
56 KRGDB ss3894121230 Apr 25, 2020 (154)
57 EVA ss3984458969 Apr 25, 2021 (155)
58 TOPMED ss4453838347 Apr 25, 2021 (155)
59 TOMMO_GENOMICS ss5144463286 Apr 25, 2021 (155)
60 1000G_HIGH_COVERAGE ss5242666805 Oct 12, 2022 (156)
61 EVA ss5319464032 Oct 12, 2022 (156)
62 HUGCELL_USP ss5443691196 Oct 12, 2022 (156)
63 EVA ss5505891487 Oct 12, 2022 (156)
64 1000G_HIGH_COVERAGE ss5515149819 Oct 12, 2022 (156)
65 SANFORD_IMAGENETICS ss5625757105 Oct 12, 2022 (156)
66 TOMMO_GENOMICS ss5669381824 Oct 12, 2022 (156)
67 YY_MCH ss5800695466 Oct 12, 2022 (156)
68 EVA ss5832113494 Oct 12, 2022 (156)
69 EVA ss5848954608 Oct 12, 2022 (156)
70 EVA ss5908720292 Oct 12, 2022 (156)
71 EVA ss5937598525 Oct 12, 2022 (156)
72 1000Genomes NC_000001.10 - 72178928 Oct 11, 2018 (152)
73 1000Genomes_30x NC_000001.11 - 71713245 Oct 12, 2022 (156)
74 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 72178928 Oct 11, 2018 (152)
75 Genetic variation in the Estonian population NC_000001.10 - 72178928 Oct 11, 2018 (152)
76 The Danish reference pan genome NC_000001.10 - 72178928 Apr 25, 2020 (154)
77 gnomAD - Genomes NC_000001.11 - 71713245 Apr 25, 2021 (155)
78 Genome of the Netherlands Release 5 NC_000001.10 - 72178928 Apr 25, 2020 (154)
79 HapMap NC_000001.11 - 71713245 Apr 25, 2020 (154)
80 KOREAN population from KRGDB NC_000001.10 - 72178928 Apr 25, 2020 (154)
81 Northern Sweden NC_000001.10 - 72178928 Jul 12, 2019 (153)
82 CNV burdens in cranial meningiomas NC_000001.10 - 72178928 Apr 25, 2021 (155)
83 Qatari NC_000001.10 - 72178928 Apr 25, 2020 (154)
84 SGDP_PRJ NC_000001.10 - 72178928 Apr 25, 2020 (154)
85 Siberian NC_000001.10 - 72178928 Apr 25, 2020 (154)
86 8.3KJPN NC_000001.10 - 72178928 Apr 25, 2021 (155)
87 14KJPN NC_000001.11 - 71713245 Oct 12, 2022 (156)
88 TopMed NC_000001.11 - 71713245 Apr 25, 2021 (155)
89 UK 10K study - Twins NC_000001.10 - 72178928 Oct 11, 2018 (152)
90 A Vietnamese Genetic Variation Database NC_000001.10 - 72178928 Jul 12, 2019 (153)
91 ALFA NC_000001.11 - 71713245 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
ss87530257, ss164526058, ss198604740, ss205203703, ss275871596, ss284070762, ss290534716, ss1584651472 NC_000001.9:71951515:G:A NC_000001.11:71713244:G:A (self)
2086418, 1144940, 810961, 1549065, 488811, 1298624, 432000, 8277, 528740, 1102614, 293892, 2432593, 1144940, 240303, ss218448245, ss230580793, ss238265955, ss648120785, ss975280009, ss1067979017, ss1291351435, ss1425848230, ss1574139515, ss1600418188, ss1643412221, ss1918486810, ss1966774301, ss2019761125, ss2147777538, ss2624393736, ss2632530811, ss2697696993, ss2756454255, ss2986999398, ss3343507078, ss3655072713, ss3727147135, ss3746344943, ss3783441912, ss3789095171, ss3793967918, ss3826230794, ss3836503263, ss3849085634, ss3894121230, ss3984458969, ss5144463286, ss5319464032, ss5505891487, ss5625757105, ss5832113494, ss5937598525 NC_000001.10:72178927:G:A NC_000001.11:71713244:G:A (self)
2675754, 14734436, 94674, 3218928, 17444682, 3272435544, ss2163465900, ss3023642595, ss3646687811, ss3686996488, ss3799350925, ss3841909985, ss4453838347, ss5242666805, ss5443691196, ss5515149819, ss5669381824, ss5800695466, ss5848954608, ss5908720292 NC_000001.11:71713244:G:A NC_000001.11:71713244:G:A (self)
ss15430512, ss18199106, ss18288070, ss19143414, ss20474026 NT_032977.6:33741996:G:A NC_000001.11:71713244:G:A (self)
ss41061898, ss97946719, ss106575253, ss137996779, ss138904684, ss155161028 NT_032977.9:42150845:G:A NC_000001.11:71713244:G:A (self)
1298624, ss3894121230 NC_000001.10:72178927:G:T NC_000001.11:71713244:G:T (self)
Help

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

1 citation for rs10789322
PMID Title Author Year Journal
25245582 Impact of NEGR1 genetic variability on psychological traits of patients with eating disorders. Gamero-Villarroel C et al. 2015 The pharmacogenomics journal
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