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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.

rs9424284

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3789974 (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
T>A / T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.324803 (85972/264690, TOPMED)
T=0.323669 (45359/140140, GnomAD)
T=0.420937 (56760/134842, ALFA) (+ 15 more)
T=0.43150 (7232/16760, 8.3KJPN)
T=0.3005 (1505/5008, 1000G)
T=0.4002 (1793/4480, Estonian)
T=0.4421 (1704/3854, ALSPAC)
T=0.4496 (1667/3708, TWINSUK)
T=0.3338 (978/2930, KOREAN)
T=0.427 (426/998, GoNL)
T=0.450 (270/600, NorthernSweden)
T=0.209 (101/484, SGDP_PRJ)
T=0.259 (83/320, HapMap)
T=0.255 (55/216, Qatari)
T=0.307 (65/212, Vietnamese)
T=0.47 (36/76, Ancient Sardinia)
T=0.22 (11/50, Siberian)
T=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.3789974T>A
GRCh38.p13 chr 1 NC_000001.11:g.3789974T>C
GRCh37.p13 chr 1 NC_000001.10:g.3706538T>A
GRCh37.p13 chr 1 NC_000001.10:g.3706538T>C
Gene: LRRC47, leucine rich repeat containing 47 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LRRC47 transcript NM_020710.3:c.616-2664A>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 134842 T=0.420937 C=0.579063
European Sub 115418 T=0.438337 C=0.561663
African Sub 5524 T=0.1133 C=0.8867
African Others Sub 208 T=0.048 C=0.952
African American Sub 5316 T=0.1159 C=0.8841
Asian Sub 622 T=0.334 C=0.666
East Asian Sub 490 T=0.331 C=0.669
Other Asian Sub 132 T=0.348 C=0.652
Latin American 1 Sub 738 T=0.327 C=0.673
Latin American 2 Sub 6250 T=0.4282 C=0.5718
South Asian Sub 184 T=0.250 C=0.750
Other Sub 6106 T=0.3883 C=0.6117


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 T=0.324803 C=0.675197
gnomAD - Genomes Global Study-wide 140140 T=0.323669 C=0.676331
gnomAD - Genomes European Sub 75866 T=0.41713 C=0.58287
gnomAD - Genomes African Sub 42030 T=0.11225 C=0.88775
gnomAD - Genomes American Sub 13642 T=0.44993 C=0.55007
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=0.3284 C=0.6716
gnomAD - Genomes East Asian Sub 3128 T=0.3261 C=0.6739
gnomAD - Genomes Other Sub 2152 T=0.3467 C=0.6533
8.3KJPN JAPANESE Study-wide 16760 T=0.43150 C=0.56850
1000Genomes Global Study-wide 5008 T=0.3005 C=0.6995
1000Genomes African Sub 1322 T=0.0522 C=0.9478
1000Genomes East Asian Sub 1008 T=0.3403 C=0.6597
1000Genomes Europe Sub 1006 T=0.4294 C=0.5706
1000Genomes South Asian Sub 978 T=0.327 C=0.673
1000Genomes American Sub 694 T=0.491 C=0.509
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.4002 C=0.5998
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.4421 C=0.5579
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.4496 C=0.5504
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.3338 A=0.0000, C=0.6662
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.427 C=0.573
Northern Sweden ACPOP Study-wide 600 T=0.450 C=0.550
SGDP_PRJ Global Study-wide 484 T=0.209 C=0.791
HapMap Global Study-wide 320 T=0.259 C=0.741
HapMap African Sub 120 T=0.025 C=0.975
HapMap American Sub 114 T=0.421 C=0.579
HapMap Asian Sub 86 T=0.37 C=0.63
Qatari Global Study-wide 216 T=0.255 C=0.745
A Vietnamese Genetic Variation Database Global Study-wide 212 T=0.307 C=0.693
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 76 T=0.47 C=0.53
Siberian Global Study-wide 50 T=0.22 C=0.78
The Danish reference pan genome Danish Study-wide 40 T=0.35 C=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 T= A C
GRCh38.p13 chr 1 NC_000001.11:g.3789974= NC_000001.11:g.3789974T>A NC_000001.11:g.3789974T>C
GRCh37.p13 chr 1 NC_000001.10:g.3706538= NC_000001.10:g.3706538T>A NC_000001.10:g.3706538T>C
LRRC47 transcript NM_020710.2:c.616-2664= NM_020710.2:c.616-2664A>T NM_020710.2:c.616-2664A>G
LRRC47 transcript NM_020710.3:c.616-2664= NM_020710.3:c.616-2664A>T NM_020710.3:c.616-2664A>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#.

88 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss12992564 Dec 05, 2003 (119)
2 SSAHASNP ss20567099 Apr 05, 2004 (121)
3 ABI ss41134670 Mar 13, 2006 (126)
4 HGSV ss82953731 Dec 14, 2007 (130)
5 BCMHGSC_JDW ss87174229 Mar 23, 2008 (129)
6 HUMANGENOME_JCVI ss97915442 Feb 04, 2009 (130)
7 BGI ss105114908 Dec 01, 2009 (131)
8 1000GENOMES ss109967097 Jan 24, 2009 (130)
9 ILLUMINA-UK ss118453396 Feb 14, 2009 (130)
10 ENSEMBL ss137763483 Dec 01, 2009 (131)
11 ENSEMBL ss138971977 Dec 01, 2009 (131)
12 ILLUMINA ss160986541 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss163004638 Jul 04, 2010 (132)
14 COMPLETE_GENOMICS ss163737583 Jul 04, 2010 (132)
15 BUSHMAN ss197924635 Jul 04, 2010 (132)
16 BCM-HGSC-SUB ss205160876 Jul 04, 2010 (132)
17 1000GENOMES ss218203192 Jul 14, 2010 (132)
18 1000GENOMES ss230404074 Jul 14, 2010 (132)
19 1000GENOMES ss238122972 Jul 15, 2010 (132)
20 BL ss252880183 May 09, 2011 (134)
21 GMI ss275691382 May 04, 2012 (137)
22 GMI ss283990983 Apr 25, 2013 (138)
23 PJP ss290498268 May 09, 2011 (134)
24 ILLUMINA ss481897495 May 04, 2012 (137)
25 ILLUMINA ss481930608 May 04, 2012 (137)
26 ILLUMINA ss482888114 Sep 08, 2015 (146)
27 ILLUMINA ss485742753 May 04, 2012 (137)
28 ILLUMINA ss537597637 Sep 08, 2015 (146)
29 TISHKOFF ss553734562 Apr 25, 2013 (138)
30 SSMP ss647536319 Apr 25, 2013 (138)
31 ILLUMINA ss778716358 Aug 21, 2014 (142)
32 ILLUMINA ss783317152 Aug 21, 2014 (142)
33 ILLUMINA ss784269145 Aug 21, 2014 (142)
34 ILLUMINA ss832578691 Apr 01, 2015 (144)
35 ILLUMINA ss834175653 Aug 21, 2014 (142)
36 EVA-GONL ss974796232 Aug 21, 2014 (142)
37 JMKIDD_LAB ss1067627157 Aug 21, 2014 (142)
38 1000GENOMES ss1289450909 Aug 21, 2014 (142)
39 DDI ss1425692909 Apr 01, 2015 (144)
40 EVA_GENOME_DK ss1573860037 Apr 01, 2015 (144)
41 EVA_DECODE ss1584155021 Apr 01, 2015 (144)
42 EVA_UK10K_ALSPAC ss1599426985 Apr 01, 2015 (144)
43 EVA_UK10K_TWINSUK ss1642421018 Apr 01, 2015 (144)
44 ILLUMINA ss1751917811 Sep 08, 2015 (146)
45 HAMMER_LAB ss1793784839 Sep 08, 2015 (146)
46 WEILL_CORNELL_DGM ss1917991773 Feb 12, 2016 (147)
47 GENOMED ss1966671325 Jul 19, 2016 (147)
48 JJLAB ss2019512005 Sep 14, 2016 (149)
49 USC_VALOUEV ss2147502400 Dec 20, 2016 (150)
50 HUMAN_LONGEVITY ss2159573042 Dec 20, 2016 (150)
51 TOPMED ss2321728006 Dec 20, 2016 (150)
52 SYSTEMSBIOZJU ss2624271760 Nov 08, 2017 (151)
53 ILLUMINA ss2632468680 Nov 08, 2017 (151)
54 GRF ss2697396411 Nov 08, 2017 (151)
55 GNOMAD ss2750970142 Nov 08, 2017 (151)
56 SWEGEN ss2986201000 Nov 08, 2017 (151)
57 BIOINF_KMB_FNS_UNIBA ss3023519630 Nov 08, 2017 (151)
58 TOPMED ss3067121845 Nov 08, 2017 (151)
59 CSHL ss3343288830 Nov 08, 2017 (151)
60 ILLUMINA ss3626011890 Oct 11, 2018 (152)
61 ILLUMINA ss3630507983 Oct 11, 2018 (152)
62 ILLUMINA ss3632878556 Oct 11, 2018 (152)
63 ILLUMINA ss3633572189 Oct 11, 2018 (152)
64 ILLUMINA ss3634303484 Oct 11, 2018 (152)
65 ILLUMINA ss3635266367 Oct 11, 2018 (152)
66 ILLUMINA ss3635979782 Oct 11, 2018 (152)
67 ILLUMINA ss3637016719 Oct 11, 2018 (152)
68 ILLUMINA ss3640010849 Oct 11, 2018 (152)
69 URBANLAB ss3646586677 Oct 11, 2018 (152)
70 EGCUT_WGS ss3654302168 Jul 12, 2019 (153)
71 EVA_DECODE ss3686046829 Jul 12, 2019 (153)
72 ACPOP ss3726739841 Jul 12, 2019 (153)
73 ILLUMINA ss3744604480 Jul 12, 2019 (153)
74 EVA ss3745755045 Jul 12, 2019 (153)
75 ILLUMINA ss3772106136 Jul 12, 2019 (153)
76 PACBIO ss3783308704 Jul 12, 2019 (153)
77 PACBIO ss3788985592 Jul 12, 2019 (153)
78 PACBIO ss3793858220 Jul 12, 2019 (153)
79 KHV_HUMAN_GENOMES ss3798776780 Jul 12, 2019 (153)
80 EVA ss3825993883 Apr 25, 2020 (154)
81 EVA ss3836384093 Apr 25, 2020 (154)
82 EVA ss3841788255 Apr 25, 2020 (154)
83 SGDP_PRJ ss3848069129 Apr 25, 2020 (154)
84 KRGDB ss3892930635 Apr 25, 2020 (154)
85 EVA ss3984774936 Apr 25, 2021 (155)
86 EVA ss4016890101 Apr 25, 2021 (155)
87 TOPMED ss4437299209 Apr 25, 2021 (155)
88 TOMMO_GENOMICS ss5142200840 Apr 25, 2021 (155)
89 1000Genomes NC_000001.10 - 3706538 Oct 11, 2018 (152)
90 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 3706538 Oct 11, 2018 (152)
91 Genetic variation in the Estonian population NC_000001.10 - 3706538 Oct 11, 2018 (152)
92 The Danish reference pan genome NC_000001.10 - 3706538 Apr 25, 2020 (154)
93 gnomAD - Genomes NC_000001.11 - 3789974 Apr 25, 2021 (155)
94 Genome of the Netherlands Release 5 NC_000001.10 - 3706538 Apr 25, 2020 (154)
95 HapMap NC_000001.11 - 3789974 Apr 25, 2020 (154)
96 KOREAN population from KRGDB NC_000001.10 - 3706538 Apr 25, 2020 (154)
97 Northern Sweden NC_000001.10 - 3706538 Jul 12, 2019 (153)
98 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 3706538 Apr 25, 2021 (155)
99 Qatari NC_000001.10 - 3706538 Apr 25, 2020 (154)
100 SGDP_PRJ NC_000001.10 - 3706538 Apr 25, 2020 (154)
101 Siberian NC_000001.10 - 3706538 Apr 25, 2020 (154)
102 8.3KJPN NC_000001.10 - 3706538 Apr 25, 2021 (155)
103 TopMed NC_000001.11 - 3789974 Apr 25, 2021 (155)
104 UK 10K study - Twins NC_000001.10 - 3706538 Oct 11, 2018 (152)
105 A Vietnamese Genetic Variation Database NC_000001.10 - 3706538 Jul 12, 2019 (153)
106 ALFA NC_000001.11 - 3789974 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)
rs57860167 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
108029, ss3892930635 NC_000001.10:3706537:T:A NC_000001.11:3789973:T:A (self)
ss82953731 NC_000001.8:3729694:T:C NC_000001.11:3789973:T:C (self)
ss87174229, ss109967097, ss118453396, ss160986541, ss163004638, ss163737583, ss197924635, ss205160876, ss252880183, ss275691382, ss283990983, ss290498268, ss481897495, ss1584155021 NC_000001.9:3696397:T:C NC_000001.11:3789973:T:C (self)
118914, 53188, 40416, 1367271, 22860, 108029, 24706, 863, 33703, 86109, 18754, 170147, 53188, 11225, ss218203192, ss230404074, ss238122972, ss481930608, ss482888114, ss485742753, ss537597637, ss553734562, ss647536319, ss778716358, ss783317152, ss784269145, ss832578691, ss834175653, ss974796232, ss1067627157, ss1289450909, ss1425692909, ss1573860037, ss1599426985, ss1642421018, ss1751917811, ss1793784839, ss1917991773, ss1966671325, ss2019512005, ss2147502400, ss2321728006, ss2624271760, ss2632468680, ss2697396411, ss2750970142, ss2986201000, ss3343288830, ss3626011890, ss3630507983, ss3632878556, ss3633572189, ss3634303484, ss3635266367, ss3635979782, ss3637016719, ss3640010849, ss3654302168, ss3726739841, ss3744604480, ss3745755045, ss3772106136, ss3783308704, ss3788985592, ss3793858220, ss3825993883, ss3836384093, ss3848069129, ss3892930635, ss3984774936, ss4016890101, ss5142200840 NC_000001.10:3706537:T:C NC_000001.11:3789973:T:C (self)
858203, 2780, 563628, 905544, 4591321590, ss2159573042, ss3023519630, ss3067121845, ss3646586677, ss3686046829, ss3798776780, ss3841788255, ss4437299209 NC_000001.11:3789973:T:C NC_000001.11:3789973:T:C (self)
ss12992564, ss20567099 NT_004321.15:1013311:T:C NC_000001.11:3789973:T:C (self)
ss41134670, ss97915442, ss105114908, ss137763483, ss138971977 NT_004350.19:3185169:T:C NC_000001.11:3789973:T:C (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 rs9424284

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