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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.

rs9633292

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:72076998 (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=0.076376 (20216/264690, TOPMED)
A=0.074053 (10052/135740, GnomAD)
A=0.18244 (5155/28256, 14KJPN) (+ 16 more)
A=0.06506 (1229/18890, ALFA)
A=0.18576 (3113/16758, 8.3KJPN)
A=0.1262 (808/6404, 1000G_30x)
A=0.1314 (658/5008, 1000G)
A=0.0645 (289/4480, Estonian)
A=0.0537 (207/3854, ALSPAC)
A=0.0515 (191/3708, TWINSUK)
A=0.2403 (704/2930, KOREAN)
A=0.2314 (424/1832, Korea1K)
A=0.055 (55/998, GoNL)
A=0.047 (28/600, NorthernSweden)
A=0.120 (26/216, Qatari)
G=0.439 (72/164, SGDP_PRJ)
A=0.05 (2/40, GENOME_DK)
G=0.5 (3/6, Siberian)
A=0.5 (3/6, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NEGR1 : 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 18890 G=0.93494 A=0.06506
European Sub 14286 G=0.94141 A=0.05859
African Sub 2946 G=0.9182 A=0.0818
African Others Sub 114 G=0.947 A=0.053
African American Sub 2832 G=0.9170 A=0.0830
Asian Sub 112 G=0.688 A=0.312
East Asian Sub 86 G=0.70 A=0.30
Other Asian Sub 26 G=0.65 A=0.35
Latin American 1 Sub 146 G=0.911 A=0.089
Latin American 2 Sub 610 G=0.957 A=0.043
South Asian Sub 98 G=0.82 A=0.18
Other Sub 692 G=0.915 A=0.085


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=0.923624 A=0.076376
gnomAD - Genomes Global Study-wide 135740 G=0.925947 A=0.074053
gnomAD - Genomes European Sub 74378 G=0.93950 A=0.06050
gnomAD - Genomes African Sub 40014 G=0.91071 A=0.08929
gnomAD - Genomes American Sub 12864 G=0.94450 A=0.05550
gnomAD - Genomes Ashkenazi Jewish Sub 3294 G=0.9463 A=0.0537
gnomAD - Genomes East Asian Sub 3108 G=0.7040 A=0.2960
gnomAD - Genomes Other Sub 2082 G=0.9193 A=0.0807
14KJPN JAPANESE Study-wide 28256 G=0.81756 A=0.18244
Allele Frequency Aggregator Total Global 18890 G=0.93494 A=0.06506
Allele Frequency Aggregator European Sub 14286 G=0.94141 A=0.05859
Allele Frequency Aggregator African Sub 2946 G=0.9182 A=0.0818
Allele Frequency Aggregator Other Sub 692 G=0.915 A=0.085
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.957 A=0.043
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.911 A=0.089
Allele Frequency Aggregator Asian Sub 112 G=0.688 A=0.312
Allele Frequency Aggregator South Asian Sub 98 G=0.82 A=0.18
8.3KJPN JAPANESE Study-wide 16758 G=0.81424 A=0.18576
1000Genomes_30x Global Study-wide 6404 G=0.8738 A=0.1262
1000Genomes_30x African Sub 1786 G=0.9076 A=0.0924
1000Genomes_30x Europe Sub 1266 G=0.9471 A=0.0529
1000Genomes_30x South Asian Sub 1202 G=0.8278 A=0.1722
1000Genomes_30x East Asian Sub 1170 G=0.7154 A=0.2846
1000Genomes_30x American Sub 980 G=0.963 A=0.037
1000Genomes Global Study-wide 5008 G=0.8686 A=0.1314
1000Genomes African Sub 1322 G=0.9107 A=0.0893
1000Genomes East Asian Sub 1008 G=0.7183 A=0.2817
1000Genomes Europe Sub 1006 G=0.9493 A=0.0507
1000Genomes South Asian Sub 978 G=0.820 A=0.180
1000Genomes American Sub 694 G=0.958 A=0.042
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9355 A=0.0645
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9463 A=0.0537
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9485 A=0.0515
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.7597 A=0.2403
Korean Genome Project KOREAN Study-wide 1832 G=0.7686 A=0.2314
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.945 A=0.055
Northern Sweden ACPOP Study-wide 600 G=0.953 A=0.047
Qatari Global Study-wide 216 G=0.880 A=0.120
SGDP_PRJ Global Study-wide 164 G=0.439 A=0.561
The Danish reference pan genome Danish Study-wide 40 G=0.95 A=0.05
Siberian Global Study-wide 6 G=0.5 A=0.5
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.72076998G>A
GRCh37.p13 chr 1 NC_000001.10:g.72542681G>A
Gene: NEGR1, neuronal growth regulator 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
NEGR1 transcript NM_173808.3:c.177-141687C…

NM_173808.3:c.177-141687C>T

N/A Intron Variant
NEGR1 transcript variant X1 XM_011541200.4:c.177-1416…

XM_011541200.4:c.177-141687C>T

N/A Intron Variant
NEGR1 transcript variant X2 XM_011541201.4:c.177-1416…

XM_011541201.4:c.177-141687C>T

N/A Intron Variant
NEGR1 transcript variant X3 XM_017000961.3:c.177-1416…

XM_017000961.3:c.177-141687C>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
GRCh38.p14 chr 1 NC_000001.11:g.72076998= NC_000001.11:g.72076998G>A
GRCh37.p13 chr 1 NC_000001.10:g.72542681= NC_000001.10:g.72542681G>A
NEGR1 transcript NM_173808.2:c.177-141687= NM_173808.2:c.177-141687C>T
NEGR1 transcript NM_173808.3:c.177-141687= NM_173808.3:c.177-141687C>T
NEGR1 transcript variant X1 XM_005270723.1:c.177-141687= XM_005270723.1:c.177-141687C>T
NEGR1 transcript variant X1 XM_011541200.4:c.177-141687= XM_011541200.4:c.177-141687C>T
NEGR1 transcript variant X2 XM_011541201.4:c.177-141687= XM_011541201.4:c.177-141687C>T
NEGR1 transcript variant X3 XM_017000961.3:c.177-141687= XM_017000961.3:c.177-141687C>T
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#.

47 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss13405666 Dec 05, 2003 (119)
2 HGSV ss80923296 Dec 14, 2007 (130)
3 COMPLETE_GENOMICS ss163504110 Jul 04, 2010 (132)
4 GMI ss275872513 May 04, 2012 (137)
5 1000GENOMES ss328688793 May 09, 2011 (134)
6 TISHKOFF ss554239663 Apr 25, 2013 (138)
7 SSMP ss648122325 Apr 25, 2013 (138)
8 EVA-GONL ss975282474 Aug 21, 2014 (142)
9 JMKIDD_LAB ss1067980819 Aug 21, 2014 (142)
10 1000GENOMES ss1291361181 Aug 21, 2014 (142)
11 EVA_GENOME_DK ss1574140905 Apr 01, 2015 (144)
12 EVA_DECODE ss1584654066 Apr 01, 2015 (144)
13 EVA_UK10K_ALSPAC ss1600423233 Apr 01, 2015 (144)
14 EVA_UK10K_TWINSUK ss1643417266 Apr 01, 2015 (144)
15 HAMMER_LAB ss1794541612 Sep 08, 2015 (146)
16 WEILL_CORNELL_DGM ss1918488988 Feb 12, 2016 (147)
17 JJLAB ss2019762399 Sep 14, 2016 (149)
18 USC_VALOUEV ss2147778781 Dec 20, 2016 (150)
19 HUMAN_LONGEVITY ss2163487690 Dec 20, 2016 (150)
20 GRF ss2697698390 Nov 08, 2017 (151)
21 GNOMAD ss2756483302 Nov 08, 2017 (151)
22 AFFY ss2985516744 Nov 08, 2017 (151)
23 SWEGEN ss2987003118 Nov 08, 2017 (151)
24 BIOINF_KMB_FNS_UNIBA ss3023643185 Nov 08, 2017 (151)
25 EGCUT_WGS ss3655076737 Jul 12, 2019 (153)
26 EVA_DECODE ss3687001305 Jul 12, 2019 (153)
27 ACPOP ss3727149209 Jul 12, 2019 (153)
28 EVA ss3746347792 Jul 12, 2019 (153)
29 KHV_HUMAN_GENOMES ss3799353745 Jul 12, 2019 (153)
30 EVA ss3826231757 Apr 25, 2020 (154)
31 SGDP_PRJ ss3849090497 Apr 25, 2020 (154)
32 KRGDB ss3894127022 Apr 25, 2020 (154)
33 KOGIC ss3944739343 Apr 25, 2020 (154)
34 TOPMED ss4453931381 Apr 25, 2021 (155)
35 TOMMO_GENOMICS ss5144474670 Apr 25, 2021 (155)
36 1000G_HIGH_COVERAGE ss5242675217 Oct 12, 2022 (156)
37 EVA ss5319480208 Oct 12, 2022 (156)
38 HUGCELL_USP ss5443699000 Oct 12, 2022 (156)
39 EVA ss5505892215 Oct 12, 2022 (156)
40 1000G_HIGH_COVERAGE ss5515163345 Oct 12, 2022 (156)
41 SANFORD_IMAGENETICS ss5625761690 Oct 12, 2022 (156)
42 TOMMO_GENOMICS ss5669396409 Oct 12, 2022 (156)
43 YY_MCH ss5800697562 Oct 12, 2022 (156)
44 EVA ss5832116467 Oct 12, 2022 (156)
45 EVA ss5848955597 Oct 12, 2022 (156)
46 EVA ss5908730045 Oct 12, 2022 (156)
47 EVA ss5937603427 Oct 12, 2022 (156)
48 1000Genomes NC_000001.10 - 72542681 Oct 11, 2018 (152)
49 1000Genomes_30x NC_000001.11 - 72076998 Oct 12, 2022 (156)
50 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 72542681 Oct 11, 2018 (152)
51 Genetic variation in the Estonian population NC_000001.10 - 72542681 Oct 11, 2018 (152)
52 The Danish reference pan genome NC_000001.10 - 72542681 Apr 25, 2020 (154)
53 gnomAD - Genomes NC_000001.11 - 72076998 Apr 25, 2021 (155)
54 Genome of the Netherlands Release 5 NC_000001.10 - 72542681 Apr 25, 2020 (154)
55 KOREAN population from KRGDB NC_000001.10 - 72542681 Apr 25, 2020 (154)
56 Korean Genome Project NC_000001.11 - 72076998 Apr 25, 2020 (154)
57 Northern Sweden NC_000001.10 - 72542681 Jul 12, 2019 (153)
58 Qatari NC_000001.10 - 72542681 Apr 25, 2020 (154)
59 SGDP_PRJ NC_000001.10 - 72542681 Apr 25, 2020 (154)
60 Siberian NC_000001.10 - 72542681 Apr 25, 2020 (154)
61 8.3KJPN NC_000001.10 - 72542681 Apr 25, 2021 (155)
62 14KJPN NC_000001.11 - 72076998 Oct 12, 2022 (156)
63 TopMed NC_000001.11 - 72076998 Apr 25, 2021 (155)
64 UK 10K study - Twins NC_000001.10 - 72542681 Oct 11, 2018 (152)
65 ALFA NC_000001.11 - 72076998 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)
rs57990072 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss80923296 NC_000001.8:72254701:G:A NC_000001.11:72076997:G:A (self)
ss163504110, ss275872513, ss1584654066 NC_000001.9:72315268:G:A NC_000001.11:72076997:G:A (self)
2096532, 1150433, 814985, 1549944, 491198, 1304416, 434074, 530918, 1107477, 295135, 2443977, 1150433, ss328688793, ss554239663, ss648122325, ss975282474, ss1067980819, ss1291361181, ss1574140905, ss1600423233, ss1643417266, ss1794541612, ss1918488988, ss2019762399, ss2147778781, ss2697698390, ss2756483302, ss2985516744, ss2987003118, ss3655076737, ss3727149209, ss3746347792, ss3826231757, ss3849090497, ss3894127022, ss5144474670, ss5319480208, ss5505892215, ss5625761690, ss5832116467, ss5937603427 NC_000001.10:72542680:G:A NC_000001.11:72076997:G:A (self)
2689280, 14810588, 1117344, 3233513, 17537716, 9681020532, ss2163487690, ss3023643185, ss3687001305, ss3799353745, ss3944739343, ss4453931381, ss5242675217, ss5443699000, ss5515163345, ss5669396409, ss5800697562, ss5848955597, ss5908730045 NC_000001.11:72076997:G:A NC_000001.11:72076997:G:A (self)
ss13405666 NT_004464.15:2987971:G:A NC_000001.11:72076997: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 rs9633292

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