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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.

rs1489396

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:78936569 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.389822 (103182/264690, TOPMED)
G=0.390534 (54631/139888, GnomAD)
G=0.37115 (7550/20342, ALFA) (+ 15 more)
G=0.29743 (4985/16760, 8.3KJPN)
G=0.3792 (1899/5008, 1000G)
G=0.3237 (1450/4480, Estonian)
G=0.3599 (1387/3854, ALSPAC)
G=0.3697 (1371/3708, TWINSUK)
G=0.2986 (875/2930, KOREAN)
G=0.2767 (507/1832, Korea1K)
G=0.4035 (711/1762, HapMap)
G=0.338 (337/998, GoNL)
G=0.452 (271/600, NorthernSweden)
G=0.244 (122/500, SGDP_PRJ)
G=0.389 (84/216, Qatari)
G=0.310 (67/216, Vietnamese)
G=0.24 (11/46, Siberian)
G=0.38 (15/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ADGRL4 : 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.78936569G>A
GRCh37.p13 chr 1 NC_000001.10:g.79402254G>A
Gene: ADGRL4, adhesion G protein-coupled receptor L4 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ADGRL4 transcript NM_022159.4:c.761-158C>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

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 20342 G=0.37115 A=0.62885
European Sub 14294 G=0.34511 A=0.65489
African Sub 4082 G=0.4814 A=0.5186
African Others Sub 144 G=0.493 A=0.507
African American Sub 3938 G=0.4810 A=0.5190
Asian Sub 116 G=0.267 A=0.733
East Asian Sub 88 G=0.24 A=0.76
Other Asian Sub 28 G=0.36 A=0.64
Latin American 1 Sub 154 G=0.409 A=0.591
Latin American 2 Sub 616 G=0.304 A=0.696
South Asian Sub 98 G=0.38 A=0.62
Other Sub 982 G=0.340 A=0.660


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=0.389822 A=0.610178
gnomAD - Genomes Global Study-wide 139888 G=0.390534 A=0.609466
gnomAD - Genomes European Sub 75782 G=0.35126 A=0.64874
gnomAD - Genomes African Sub 41888 G=0.48088 A=0.51912
gnomAD - Genomes American Sub 13624 G=0.35335 A=0.64665
gnomAD - Genomes Ashkenazi Jewish Sub 3318 G=0.3867 A=0.6133
gnomAD - Genomes East Asian Sub 3126 G=0.3049 A=0.6951
gnomAD - Genomes Other Sub 2150 G=0.3809 A=0.6191
8.3KJPN JAPANESE Study-wide 16760 G=0.29743 A=0.70257
1000Genomes Global Study-wide 5008 G=0.3792 A=0.6208
1000Genomes African Sub 1322 G=0.5061 A=0.4939
1000Genomes East Asian Sub 1008 G=0.2956 A=0.7044
1000Genomes Europe Sub 1006 G=0.3807 A=0.6193
1000Genomes South Asian Sub 978 G=0.337 A=0.663
1000Genomes American Sub 694 G=0.316 A=0.684
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.3237 A=0.6763
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.3599 A=0.6401
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.3697 A=0.6303
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.2986 A=0.7014
Korean Genome Project KOREAN Study-wide 1832 G=0.2767 A=0.7233
HapMap Global Study-wide 1762 G=0.4035 A=0.5965
HapMap African Sub 670 G=0.543 A=0.457
HapMap American Sub 666 G=0.326 A=0.674
HapMap Asian Sub 252 G=0.258 A=0.742
HapMap Europe Sub 174 G=0.374 A=0.626
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.338 A=0.662
Northern Sweden ACPOP Study-wide 600 G=0.452 A=0.548
SGDP_PRJ Global Study-wide 500 G=0.244 A=0.756
Qatari Global Study-wide 216 G=0.389 A=0.611
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.310 A=0.690
Siberian Global Study-wide 46 G=0.24 A=0.76
The Danish reference pan genome Danish Study-wide 40 G=0.38 A=0.62
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.p13 chr 1 NC_000001.11:g.78936569= NC_000001.11:g.78936569G>A
GRCh37.p13 chr 1 NC_000001.10:g.79402254= NC_000001.10:g.79402254G>A
ADGRL4 transcript NM_022159.3:c.761-158= NM_022159.3:c.761-158C>T
ADGRL4 transcript NM_022159.4:c.761-158= NM_022159.4:c.761-158C>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#.

69 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2315076 Oct 23, 2000 (88)
2 BCM_SSAHASNP ss9841858 Jul 11, 2003 (116)
3 PERLEGEN ss46536147 Mar 15, 2006 (126)
4 ILLUMINA ss65715861 Oct 13, 2006 (127)
5 ILLUMINA ss74861741 Dec 07, 2007 (129)
6 HGSV ss84371318 Dec 15, 2007 (130)
7 BCMHGSC_JDW ss87562655 Mar 23, 2008 (129)
8 BGI ss106579489 Feb 05, 2009 (130)
9 1000GENOMES ss108338188 Jan 23, 2009 (130)
10 ILLUMINA-UK ss118830204 Feb 14, 2009 (130)
11 KRIBB_YJKIM ss119395147 Dec 01, 2009 (131)
12 ILLUMINA ss120244570 Dec 01, 2009 (131)
13 ENSEMBL ss138014034 Dec 01, 2009 (131)
14 GMI ss155226900 Dec 01, 2009 (131)
15 ILLUMINA ss172537814 Jul 04, 2010 (132)
16 BUSHMAN ss198664114 Jul 04, 2010 (132)
17 1000GENOMES ss210565338 Jul 14, 2010 (132)
18 1000GENOMES ss218474244 Jul 14, 2010 (132)
19 1000GENOMES ss230599666 Jul 14, 2010 (132)
20 1000GENOMES ss238279821 Jul 15, 2010 (132)
21 ILLUMINA ss244255346 Jul 04, 2010 (132)
22 GMI ss275889840 May 04, 2012 (137)
23 GMI ss284079591 Apr 25, 2013 (138)
24 PJP ss290544555 May 09, 2011 (134)
25 ILLUMINA ss536880923 Sep 08, 2015 (146)
26 SSMP ss648153124 Apr 25, 2013 (138)
27 EVA-GONL ss975331459 Aug 21, 2014 (142)
28 JMKIDD_LAB ss1068017879 Aug 21, 2014 (142)
29 1000GENOMES ss1291546975 Aug 21, 2014 (142)
30 DDI ss1425864861 Apr 01, 2015 (144)
31 EVA_GENOME_DK ss1574171675 Apr 01, 2015 (144)
32 EVA_DECODE ss1584704816 Apr 01, 2015 (144)
33 EVA_UK10K_ALSPAC ss1600518939 Apr 01, 2015 (144)
34 EVA_UK10K_TWINSUK ss1643512972 Apr 01, 2015 (144)
35 EVA_SVP ss1712346029 Apr 01, 2015 (144)
36 WEILL_CORNELL_DGM ss1918535392 Feb 12, 2016 (147)
37 GENOMED ss1966786432 Jul 19, 2016 (147)
38 JJLAB ss2019788170 Sep 14, 2016 (149)
39 USC_VALOUEV ss2147803902 Dec 20, 2016 (150)
40 HUMAN_LONGEVITY ss2163878571 Dec 20, 2016 (150)
41 TOPMED ss2326162993 Dec 20, 2016 (150)
42 SYSTEMSBIOZJU ss2624404741 Nov 08, 2017 (151)
43 GRF ss2697724077 Nov 08, 2017 (151)
44 GNOMAD ss2757021920 Nov 08, 2017 (151)
45 SWEGEN ss2987075492 Nov 08, 2017 (151)
46 BIOINF_KMB_FNS_UNIBA ss3023655977 Nov 08, 2017 (151)
47 TOPMED ss3080952958 Nov 08, 2017 (151)
48 CSHL ss3343528653 Nov 08, 2017 (151)
49 ILLUMINA ss3626133916 Oct 11, 2018 (152)
50 ILLUMINA ss3637766755 Oct 11, 2018 (152)
51 ILLUMINA ss3642777760 Oct 11, 2018 (152)
52 URBANLAB ss3646698691 Oct 11, 2018 (152)
53 EGCUT_WGS ss3655154022 Jul 12, 2019 (153)
54 EVA_DECODE ss3687090810 Jul 12, 2019 (153)
55 ACPOP ss3727189171 Jul 12, 2019 (153)
56 EVA ss3746402209 Jul 12, 2019 (153)
57 PACBIO ss3783455235 Jul 12, 2019 (153)
58 PACBIO ss3789106583 Jul 12, 2019 (153)
59 PACBIO ss3793979334 Jul 12, 2019 (153)
60 KHV_HUMAN_GENOMES ss3799407842 Jul 12, 2019 (153)
61 EVA ss3826254623 Apr 25, 2020 (154)
62 EVA ss3836515565 Apr 25, 2020 (154)
63 EVA ss3841922560 Apr 25, 2020 (154)
64 SGDP_PRJ ss3849185349 Apr 25, 2020 (154)
65 KRGDB ss3894232470 Apr 25, 2020 (154)
66 KOGIC ss3944824581 Apr 25, 2020 (154)
67 EVA ss4016919591 Apr 25, 2021 (155)
68 TOPMED ss4455625644 Apr 25, 2021 (155)
69 TOMMO_GENOMICS ss5144677536 Apr 25, 2021 (155)
70 1000Genomes NC_000001.10 - 79402254 Oct 11, 2018 (152)
71 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 79402254 Oct 11, 2018 (152)
72 Genetic variation in the Estonian population NC_000001.10 - 79402254 Oct 11, 2018 (152)
73 The Danish reference pan genome NC_000001.10 - 79402254 Apr 25, 2020 (154)
74 gnomAD - Genomes NC_000001.11 - 78936569 Apr 25, 2021 (155)
75 Genome of the Netherlands Release 5 NC_000001.10 - 79402254 Apr 25, 2020 (154)
76 HapMap NC_000001.11 - 78936569 Apr 25, 2020 (154)
77 KOREAN population from KRGDB NC_000001.10 - 79402254 Apr 25, 2020 (154)
78 Korean Genome Project NC_000001.11 - 78936569 Apr 25, 2020 (154)
79 Northern Sweden NC_000001.10 - 79402254 Jul 12, 2019 (153)
80 Qatari NC_000001.10 - 79402254 Apr 25, 2020 (154)
81 SGDP_PRJ NC_000001.10 - 79402254 Apr 25, 2020 (154)
82 Siberian NC_000001.10 - 79402254 Apr 25, 2020 (154)
83 8.3KJPN NC_000001.10 - 79402254 Apr 25, 2021 (155)
84 TopMed NC_000001.11 - 78936569 Apr 25, 2021 (155)
85 UK 10K study - Twins NC_000001.10 - 79402254 Oct 11, 2018 (152)
86 A Vietnamese Genetic Variation Database NC_000001.10 - 79402254 Jul 12, 2019 (153)
87 ALFA NC_000001.11 - 78936569 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)
rs59935328 May 25, 2008 (130)
rs386534154 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss84371318 NC_000001.8:79114274:G:A NC_000001.11:78936568:G:A (self)
ss87562655, ss108338188, ss118830204, ss198664114, ss210565338, ss275889840, ss284079591, ss290544555, ss1584704816, ss1712346029, ss3642777760 NC_000001.9:79174841:G:A NC_000001.11:78936568:G:A (self)
2289314, 1255622, 892270, 1569469, 539127, 1409864, 474036, 577322, 1202329, 320256, 2646843, 1255622, 266113, ss218474244, ss230599666, ss238279821, ss536880923, ss648153124, ss975331459, ss1068017879, ss1291546975, ss1425864861, ss1574171675, ss1600518939, ss1643512972, ss1918535392, ss1966786432, ss2019788170, ss2147803902, ss2326162993, ss2624404741, ss2697724077, ss2757021920, ss2987075492, ss3343528653, ss3626133916, ss3637766755, ss3655154022, ss3727189171, ss3746402209, ss3783455235, ss3789106583, ss3793979334, ss3826254623, ss3836515565, ss3849185349, ss3894232470, ss4016919591, ss5144677536 NC_000001.10:79402253:G:A NC_000001.11:78936568:G:A (self)
16181858, 105606, 1202582, 12112178, 19231979, 2745885609, ss2163878571, ss3023655977, ss3080952958, ss3646698691, ss3687090810, ss3799407842, ss3841922560, ss3944824581, ss4455625644 NC_000001.11:78936568:G:A NC_000001.11:78936568:G:A (self)
ss9841858 NT_004483.15:1071324:G:A NC_000001.11:78936568:G:A (self)
ss2315076, ss46536147, ss65715861, ss74861741, ss106579489, ss119395147, ss120244570, ss138014034, ss155226900, ss172537814, ss244255346 NT_032977.9:49374171:G:A NC_000001.11:78936568: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 rs1489396

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