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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.

rs9424283

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3788662 (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
C>G
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.324995 (86023/264690, TOPMED)
C=0.325841 (45591/139918, GnomAD)
C=0.36702 (6933/18890, ALFA) (+ 13 more)
C=0.43156 (7233/16760, 8.3KJPN)
C=0.3011 (1508/5008, 1000G)
C=0.4408 (1699/3854, ALSPAC)
C=0.4493 (1666/3708, TWINSUK)
C=0.3337 (977/2928, KOREAN)
C=0.2638 (496/1880, HapMap)
C=0.427 (426/998, GoNL)
C=0.460 (276/600, NorthernSweden)
C=0.212 (102/482, SGDP_PRJ)
C=0.255 (55/216, Qatari)
C=0.305 (64/210, Vietnamese)
C=0.22 (11/50, Siberian)
C=0.35 (14/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LRRC47 : 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.3788662C>G
GRCh37.p13 chr 1 NC_000001.10:g.3705226C>G
Gene: LRRC47, leucine rich repeat containing 47 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LRRC47 transcript NM_020710.3:c.616-1352G>C 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 18890 C=0.36702 G=0.63298
European Sub 14286 C=0.42265 G=0.57735
African Sub 2946 C=0.1025 G=0.8975
African Others Sub 114 C=0.035 G=0.965
African American Sub 2832 C=0.1052 G=0.8948
Asian Sub 112 C=0.348 G=0.652
East Asian Sub 86 C=0.30 G=0.70
Other Asian Sub 26 C=0.50 G=0.50
Latin American 1 Sub 146 C=0.301 G=0.699
Latin American 2 Sub 610 C=0.405 G=0.595
South Asian Sub 98 C=0.26 G=0.74
Other Sub 692 C=0.344 G=0.656


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 C=0.324995 G=0.675005
gnomAD - Genomes Global Study-wide 139918 C=0.325841 G=0.674159
gnomAD - Genomes European Sub 75774 C=0.42123 G=0.57877
gnomAD - Genomes African Sub 41944 C=0.11241 G=0.88759
gnomAD - Genomes American Sub 13610 C=0.44871 G=0.55129
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.3284 G=0.6716
gnomAD - Genomes East Asian Sub 3122 C=0.3251 G=0.6749
gnomAD - Genomes Other Sub 2146 C=0.3472 G=0.6528
8.3KJPN JAPANESE Study-wide 16760 C=0.43156 G=0.56844
1000Genomes Global Study-wide 5008 C=0.3011 G=0.6989
1000Genomes African Sub 1322 C=0.0522 G=0.9478
1000Genomes East Asian Sub 1008 C=0.3423 G=0.6577
1000Genomes Europe Sub 1006 C=0.4314 G=0.5686
1000Genomes South Asian Sub 978 C=0.327 G=0.673
1000Genomes American Sub 694 C=0.490 G=0.510
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.4408 G=0.5592
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.4493 G=0.5507
KOREAN population from KRGDB KOREAN Study-wide 2928 C=0.3337 G=0.6663
HapMap Global Study-wide 1880 C=0.2638 G=0.7362
HapMap American Sub 762 C=0.375 G=0.625
HapMap African Sub 690 C=0.061 G=0.939
HapMap Asian Sub 254 C=0.398 G=0.602
HapMap Europe Sub 174 C=0.385 G=0.615
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.427 G=0.573
Northern Sweden ACPOP Study-wide 600 C=0.460 G=0.540
SGDP_PRJ Global Study-wide 482 C=0.212 G=0.788
Qatari Global Study-wide 216 C=0.255 G=0.745
A Vietnamese Genetic Variation Database Global Study-wide 210 C=0.305 G=0.695
Siberian Global Study-wide 50 C=0.22 G=0.78
The Danish reference pan genome Danish Study-wide 40 C=0.35 G=0.65
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 C= G
GRCh38.p13 chr 1 NC_000001.11:g.3788662= NC_000001.11:g.3788662C>G
GRCh37.p13 chr 1 NC_000001.10:g.3705226= NC_000001.10:g.3705226C>G
LRRC47 transcript NM_020710.2:c.616-1352= NM_020710.2:c.616-1352G>C
LRRC47 transcript NM_020710.3:c.616-1352= NM_020710.3:c.616-1352G>C
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#.

67 SubSNP, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss12992563 Dec 05, 2003 (119)
2 SSAHASNP ss20608198 Apr 05, 2004 (121)
3 PERLEGEN ss24243484 Sep 20, 2004 (123)
4 ABI ss44125209 Mar 14, 2006 (126)
5 AFFY ss66362339 Nov 29, 2006 (127)
6 AFFY ss76081926 Dec 08, 2007 (130)
7 HGSV ss77767017 Dec 07, 2007 (129)
8 KRIBB_YJKIM ss82580804 Dec 16, 2007 (130)
9 BCMHGSC_JDW ss87174219 Mar 23, 2008 (129)
10 HUMANGENOME_JCVI ss97915440 Feb 04, 2009 (130)
11 BGI ss105114905 Dec 01, 2009 (131)
12 1000GENOMES ss107948943 Jan 22, 2009 (130)
13 1000GENOMES ss109967081 Jan 24, 2009 (130)
14 ILLUMINA-UK ss118453388 Feb 14, 2009 (130)
15 ENSEMBL ss137763479 Dec 01, 2009 (131)
16 ENSEMBL ss139812761 Dec 01, 2009 (131)
17 COMPLETE_GENOMICS ss163004634 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss163737553 Jul 04, 2010 (132)
19 AFFY ss172439059 Jul 04, 2010 (132)
20 BUSHMAN ss197924591 Jul 04, 2010 (132)
21 BCM-HGSC-SUB ss205112296 Jul 04, 2010 (132)
22 1000GENOMES ss218203185 Jul 14, 2010 (132)
23 1000GENOMES ss230404067 Jul 14, 2010 (132)
24 1000GENOMES ss238122965 Jul 15, 2010 (132)
25 BL ss252880171 May 09, 2011 (134)
26 GMI ss275691379 May 04, 2012 (137)
27 GMI ss283990980 Apr 25, 2013 (138)
28 PJP ss290498263 May 09, 2011 (134)
29 TISHKOFF ss553734553 Apr 25, 2013 (138)
30 SSMP ss647536306 Apr 25, 2013 (138)
31 EVA-GONL ss974796218 Aug 21, 2014 (142)
32 JMKIDD_LAB ss1067627145 Aug 21, 2014 (142)
33 1000GENOMES ss1289450855 Aug 21, 2014 (142)
34 DDI ss1425692902 Apr 01, 2015 (144)
35 EVA_GENOME_DK ss1573860027 Apr 01, 2015 (144)
36 EVA_DECODE ss1584155002 Apr 01, 2015 (144)
37 EVA_UK10K_ALSPAC ss1599426954 Apr 01, 2015 (144)
38 EVA_UK10K_TWINSUK ss1642420987 Apr 01, 2015 (144)
39 EVA_SVP ss1712306763 Apr 01, 2015 (144)
40 HAMMER_LAB ss1793784834 Sep 08, 2015 (146)
41 WEILL_CORNELL_DGM ss1917991753 Feb 12, 2016 (147)
42 JJLAB ss2019511994 Sep 14, 2016 (149)
43 USC_VALOUEV ss2147502394 Dec 20, 2016 (150)
44 HUMAN_LONGEVITY ss2159572931 Dec 20, 2016 (150)
45 TOPMED ss2321727889 Dec 20, 2016 (150)
46 SYSTEMSBIOZJU ss2624271754 Nov 08, 2017 (151)
47 GRF ss2697396401 Nov 08, 2017 (151)
48 GNOMAD ss2750970007 Nov 08, 2017 (151)
49 SWEGEN ss2986200980 Nov 08, 2017 (151)
50 BIOINF_KMB_FNS_UNIBA ss3023519625 Nov 08, 2017 (151)
51 TOPMED ss3067121553 Nov 08, 2017 (151)
52 CSHL ss3343288820 Nov 08, 2017 (151)
53 URBANLAB ss3646586673 Oct 11, 2018 (152)
54 EVA_DECODE ss3686046801 Jul 12, 2019 (153)
55 ACPOP ss3726739826 Jul 12, 2019 (153)
56 EVA ss3745755019 Jul 12, 2019 (153)
57 PACBIO ss3783308701 Jul 12, 2019 (153)
58 PACBIO ss3788985589 Jul 12, 2019 (153)
59 PACBIO ss3793858217 Jul 12, 2019 (153)
60 KHV_HUMAN_GENOMES ss3798776763 Jul 12, 2019 (153)
61 EVA ss3825993878 Apr 25, 2020 (154)
62 EVA ss3836384090 Apr 25, 2020 (154)
63 EVA ss3841788252 Apr 25, 2020 (154)
64 SGDP_PRJ ss3848069102 Apr 25, 2020 (154)
65 KRGDB ss3892930606 Apr 25, 2020 (154)
66 TOPMED ss4437298795 Apr 25, 2021 (155)
67 TOMMO_GENOMICS ss5142200791 Apr 25, 2021 (155)
68 1000Genomes NC_000001.10 - 3705226 Oct 11, 2018 (152)
69 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 3705226 Oct 11, 2018 (152)
70 The Danish reference pan genome NC_000001.10 - 3705226 Apr 25, 2020 (154)
71 gnomAD - Genomes NC_000001.11 - 3788662 Apr 25, 2021 (155)
72 Genome of the Netherlands Release 5 NC_000001.10 - 3705226 Apr 25, 2020 (154)
73 HapMap NC_000001.11 - 3788662 Apr 25, 2020 (154)
74 KOREAN population from KRGDB NC_000001.10 - 3705226 Apr 25, 2020 (154)
75 Northern Sweden NC_000001.10 - 3705226 Jul 12, 2019 (153)
76 Qatari NC_000001.10 - 3705226 Apr 25, 2020 (154)
77 SGDP_PRJ NC_000001.10 - 3705226 Apr 25, 2020 (154)
78 Siberian NC_000001.10 - 3705226 Apr 25, 2020 (154)
79 8.3KJPN NC_000001.10 - 3705226 Apr 25, 2021 (155)
80 TopMed NC_000001.11 - 3788662 Apr 25, 2021 (155)
81 UK 10K study - Twins NC_000001.10 - 3705226 Oct 11, 2018 (152)
82 A Vietnamese Genetic Variation Database NC_000001.10 - 3705226 Jul 12, 2019 (153)
83 ALFA NC_000001.11 - 3788662 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)
rs17402949 Oct 07, 2004 (123)
rs56573322 May 24, 2008 (130)
rs61325893 Feb 26, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77767017 NC_000001.8:3728382:C:G NC_000001.11:3788661:C:G (self)
ss66362339, ss76081926, ss87174219, ss107948943, ss109967081, ss118453388, ss163004634, ss163737553, ss172439059, ss197924591, ss205112296, ss252880171, ss275691379, ss283990980, ss290498263, ss1584155002, ss1712306763 NC_000001.9:3695085:C:G NC_000001.11:3788661:C:G (self)
118860, 53157, 1367261, 22846, 108000, 24691, 33683, 86082, 18748, 170098, 53157, 11218, ss218203185, ss230404067, ss238122965, ss553734553, ss647536306, ss974796218, ss1067627145, ss1289450855, ss1425692902, ss1573860027, ss1599426954, ss1642420987, ss1793784834, ss1917991753, ss2019511994, ss2147502394, ss2321727889, ss2624271754, ss2697396401, ss2750970007, ss2986200980, ss3343288820, ss3726739826, ss3745755019, ss3783308701, ss3788985589, ss3793858217, ss3825993878, ss3836384090, ss3848069102, ss3892930606, ss5142200791 NC_000001.10:3705225:C:G NC_000001.11:3788661:C:G (self)
857891, 2777, 563365, 905130, 3014389249, ss2159572931, ss3023519625, ss3067121553, ss3646586673, ss3686046801, ss3798776763, ss3841788252, ss4437298795 NC_000001.11:3788661:C:G NC_000001.11:3788661:C:G (self)
ss12992563, ss20608198 NT_004321.15:1011999:C:G NC_000001.11:3788661:C:G (self)
ss24243484, ss44125209, ss82580804, ss97915440, ss105114905, ss137763479, ss139812761 NT_004350.19:3183857:C:G NC_000001.11:3788661:C: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 rs9424283

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