Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs9424282

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3788457 (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 / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.431505 (114215/264690, TOPMED)
C=0.417931 (58471/139906, GnomAD)
C=0.36195 (6652/18378, ALFA) (+ 13 more)
T=0.43121 (7227/16760, 8.3KJPN)
T=0.4962 (2485/5008, 1000G)
C=0.3335 (1494/4480, Estonian)
C=0.2989 (1152/3854, ALSPAC)
C=0.2994 (1110/3708, TWINSUK)
T=0.3341 (979/2930, KOREAN)
C=0.311 (310/998, GoNL)
C=0.353 (212/600, NorthernSweden)
T=0.318 (126/396, SGDP_PRJ)
T=0.458 (99/216, Qatari)
T=0.332 (71/214, Vietnamese)
C=0.45 (18/40, GENOME_DK)
T=0.29 (11/38, Siberian)
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.3788457T>A
GRCh38.p13 chr 1 NC_000001.11:g.3788457T>C
GRCh38.p13 chr 1 NC_000001.11:g.3788457T>G
GRCh37.p13 chr 1 NC_000001.10:g.3705021T>A
GRCh37.p13 chr 1 NC_000001.10:g.3705021T>C
GRCh37.p13 chr 1 NC_000001.10:g.3705021T>G
Gene: LRRC47, leucine rich repeat containing 47 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LRRC47 transcript NM_020710.3:c.616-1147A>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 18378 T=0.63805 C=0.36195, G=0.00000
European Sub 13908 T=0.68745 C=0.31255, G=0.00000
African Sub 2538 T=0.4322 C=0.5678, G=0.0000
African Others Sub 96 T=0.35 C=0.65, G=0.00
African American Sub 2442 T=0.4353 C=0.5647, G=0.0000
Asian Sub 116 T=0.353 C=0.647, G=0.000
East Asian Sub 88 T=0.31 C=0.69, G=0.00
Other Asian Sub 28 T=0.50 C=0.50, G=0.00
Latin American 1 Sub 154 T=0.526 C=0.474, G=0.000
Latin American 2 Sub 616 T=0.557 C=0.443, G=0.000
South Asian Sub 98 T=0.40 C=0.60, G=0.00
Other Sub 948 T=0.595 C=0.405, G=0.000


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=0.568495 C=0.431505
gnomAD - Genomes Global Study-wide 139906 T=0.582069 C=0.417931
gnomAD - Genomes European Sub 75778 T=0.68169 C=0.31831
gnomAD - Genomes African Sub 41904 T=0.40075 C=0.59925
gnomAD - Genomes American Sub 13642 T=0.62593 C=0.37407
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=0.6484 C=0.3516
gnomAD - Genomes East Asian Sub 3114 T=0.3317 C=0.6683
gnomAD - Genomes Other Sub 2146 T=0.5867 C=0.4133
Allele Frequency Aggregator Total Global 18378 T=0.63805 C=0.36195, G=0.00000
Allele Frequency Aggregator European Sub 13908 T=0.68745 C=0.31255, G=0.00000
Allele Frequency Aggregator African Sub 2538 T=0.4322 C=0.5678, G=0.0000
Allele Frequency Aggregator Other Sub 948 T=0.595 C=0.405, G=0.000
Allele Frequency Aggregator Latin American 2 Sub 616 T=0.557 C=0.443, G=0.000
Allele Frequency Aggregator Latin American 1 Sub 154 T=0.526 C=0.474, G=0.000
Allele Frequency Aggregator Asian Sub 116 T=0.353 C=0.647, G=0.000
Allele Frequency Aggregator South Asian Sub 98 T=0.40 C=0.60, G=0.00
8.3KJPN JAPANESE Study-wide 16760 T=0.43121 C=0.56879
1000Genomes Global Study-wide 5008 T=0.4962 C=0.5038
1000Genomes African Sub 1322 T=0.3775 C=0.6225
1000Genomes East Asian Sub 1008 T=0.3433 C=0.6567
1000Genomes Europe Sub 1006 T=0.6501 C=0.3499
1000Genomes South Asian Sub 978 T=0.551 C=0.449
1000Genomes American Sub 694 T=0.644 C=0.356
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.6665 C=0.3335
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.7011 C=0.2989
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.7006 C=0.2994
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.3341 A=0.0000, C=0.6659, G=0.0000
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.689 C=0.311
Northern Sweden ACPOP Study-wide 600 T=0.647 C=0.353
SGDP_PRJ Global Study-wide 396 T=0.318 C=0.682
Qatari Global Study-wide 216 T=0.458 C=0.542
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.332 C=0.668
The Danish reference pan genome Danish Study-wide 40 T=0.55 C=0.45
Siberian Global Study-wide 38 T=0.29 C=0.71
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 G
GRCh38.p13 chr 1 NC_000001.11:g.3788457= NC_000001.11:g.3788457T>A NC_000001.11:g.3788457T>C NC_000001.11:g.3788457T>G
GRCh37.p13 chr 1 NC_000001.10:g.3705021= NC_000001.10:g.3705021T>A NC_000001.10:g.3705021T>C NC_000001.10:g.3705021T>G
LRRC47 transcript NM_020710.2:c.616-1147= NM_020710.2:c.616-1147A>T NM_020710.2:c.616-1147A>G NM_020710.2:c.616-1147A>C
LRRC47 transcript NM_020710.3:c.616-1147= NM_020710.3:c.616-1147A>T NM_020710.3:c.616-1147A>G NM_020710.3:c.616-1147A>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#.

62 SubSNP, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss12992562 Dec 05, 2003 (119)
2 CSHL-HAPMAP ss19868035 Feb 27, 2004 (120)
3 SSAHASNP ss20518462 Apr 05, 2004 (121)
4 ABI ss44031829 Mar 15, 2006 (126)
5 HGSV ss77819145 Dec 07, 2007 (129)
6 HUMANGENOME_JCVI ss97915439 Feb 05, 2009 (130)
7 BGI ss105114903 Dec 01, 2009 (131)
8 1000GENOMES ss109967076 Jan 24, 2009 (130)
9 ENSEMBL ss138972028 Dec 01, 2009 (131)
10 COMPLETE_GENOMICS ss163004629 Jul 04, 2010 (132)
11 COMPLETE_GENOMICS ss163737523 Jul 04, 2010 (132)
12 BUSHMAN ss197924586 Jul 04, 2010 (132)
13 BCM-HGSC-SUB ss205232691 Jul 04, 2010 (132)
14 1000GENOMES ss218203183 Jul 14, 2010 (132)
15 1000GENOMES ss230404064 Jul 14, 2010 (132)
16 1000GENOMES ss238122963 Jul 15, 2010 (132)
17 BL ss252880159 May 09, 2011 (134)
18 GMI ss275691377 May 04, 2012 (137)
19 GMI ss283990978 Apr 25, 2013 (138)
20 PJP ss290498261 May 09, 2011 (134)
21 ILLUMINA ss536043951 Sep 08, 2015 (146)
22 TISHKOFF ss553734550 Apr 25, 2013 (138)
23 SSMP ss647536303 Apr 25, 2013 (138)
24 EVA-GONL ss974796214 Aug 21, 2014 (142)
25 JMKIDD_LAB ss1067627142 Aug 21, 2014 (142)
26 1000GENOMES ss1289450848 Aug 21, 2014 (142)
27 DDI ss1425692901 Apr 01, 2015 (144)
28 EVA_GENOME_DK ss1573860025 Apr 01, 2015 (144)
29 EVA_DECODE ss1584154999 Apr 01, 2015 (144)
30 EVA_UK10K_ALSPAC ss1599426949 Apr 01, 2015 (144)
31 EVA_UK10K_TWINSUK ss1642420982 Apr 01, 2015 (144)
32 HAMMER_LAB ss1793784831 Sep 08, 2015 (146)
33 WEILL_CORNELL_DGM ss1917991750 Feb 12, 2016 (147)
34 GENOMED ss1966671320 Jul 19, 2016 (147)
35 JJLAB ss2019511991 Sep 14, 2016 (149)
36 USC_VALOUEV ss2147502392 Dec 20, 2016 (150)
37 HUMAN_LONGEVITY ss2159572918 Dec 20, 2016 (150)
38 TOPMED ss2321727875 Dec 20, 2016 (150)
39 SYSTEMSBIOZJU ss2624271752 Nov 08, 2017 (151)
40 GRF ss2697396399 Nov 08, 2017 (151)
41 GNOMAD ss2750969986 Nov 08, 2017 (151)
42 SWEGEN ss2986200976 Nov 08, 2017 (151)
43 BIOINF_KMB_FNS_UNIBA ss3023519622 Nov 08, 2017 (151)
44 TOPMED ss3067121511 Nov 08, 2017 (151)
45 CSHL ss3343288817 Nov 08, 2017 (151)
46 ILLUMINA ss3626011884 Oct 11, 2018 (152)
47 URBANLAB ss3646586672 Oct 11, 2018 (152)
48 EGCUT_WGS ss3654302147 Jul 12, 2019 (153)
49 EVA_DECODE ss3686046798 Jul 12, 2019 (153)
50 ACPOP ss3726739823 Jul 12, 2019 (153)
51 EVA ss3745755016 Jul 12, 2019 (153)
52 PACBIO ss3783308698 Jul 12, 2019 (153)
53 PACBIO ss3788985586 Jul 12, 2019 (153)
54 PACBIO ss3793858214 Jul 12, 2019 (153)
55 KHV_HUMAN_GENOMES ss3798776759 Jul 12, 2019 (153)
56 EVA ss3825993877 Apr 25, 2020 (154)
57 EVA ss3836384087 Apr 25, 2020 (154)
58 EVA ss3841788249 Apr 25, 2020 (154)
59 SGDP_PRJ ss3848069096 Apr 25, 2020 (154)
60 KRGDB ss3892930599 Apr 25, 2020 (154)
61 TOPMED ss4437298747 Apr 25, 2021 (155)
62 TOMMO_GENOMICS ss5142200785 Apr 25, 2021 (155)
63 1000Genomes NC_000001.10 - 3705021 Oct 11, 2018 (152)
64 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 3705021 Oct 11, 2018 (152)
65 Genetic variation in the Estonian population NC_000001.10 - 3705021 Oct 11, 2018 (152)
66 The Danish reference pan genome NC_000001.10 - 3705021 Apr 25, 2020 (154)
67 gnomAD - Genomes NC_000001.11 - 3788457 Apr 25, 2021 (155)
68 Genome of the Netherlands Release 5 NC_000001.10 - 3705021 Apr 25, 2020 (154)
69 KOREAN population from KRGDB NC_000001.10 - 3705021 Apr 25, 2020 (154)
70 Northern Sweden NC_000001.10 - 3705021 Jul 12, 2019 (153)
71 Qatari NC_000001.10 - 3705021 Apr 25, 2020 (154)
72 SGDP_PRJ NC_000001.10 - 3705021 Apr 25, 2020 (154)
73 Siberian NC_000001.10 - 3705021 Apr 25, 2020 (154)
74 8.3KJPN NC_000001.10 - 3705021 Apr 25, 2021 (155)
75 TopMed NC_000001.11 - 3788457 Apr 25, 2021 (155)
76 UK 10K study - Twins NC_000001.10 - 3705021 Oct 11, 2018 (152)
77 A Vietnamese Genetic Variation Database NC_000001.10 - 3705021 Jul 12, 2019 (153)
78 ALFA NC_000001.11 - 3788457 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
107993, ss3892930599 NC_000001.10:3705020:T:A NC_000001.11:3788456:T:A (self)
ss77819145 NC_000001.8:3728177:T:C NC_000001.11:3788456:T:C (self)
ss109967076, ss163004629, ss163737523, ss197924586, ss205232691, ss252880159, ss275691377, ss283990978, ss290498261, ss1584154999 NC_000001.9:3694880:T:C NC_000001.11:3788456:T:C (self)
118853, 53152, 40395, 1367259, 22842, 107993, 24688, 33680, 86076, 18746, 170092, 53152, 11214, ss218203183, ss230404064, ss238122963, ss536043951, ss553734550, ss647536303, ss974796214, ss1067627142, ss1289450848, ss1425692901, ss1573860025, ss1599426949, ss1642420982, ss1793784831, ss1917991750, ss1966671320, ss2019511991, ss2147502392, ss2321727875, ss2624271752, ss2697396399, ss2750969986, ss2986200976, ss3343288817, ss3626011884, ss3654302147, ss3726739823, ss3745755016, ss3783308698, ss3788985586, ss3793858214, ss3825993877, ss3836384087, ss3848069096, ss3892930599, ss5142200785 NC_000001.10:3705020:T:C NC_000001.11:3788456:T:C (self)
857849, 563327, 905082, 1782334708, ss2159572918, ss3023519622, ss3067121511, ss3646586672, ss3686046798, ss3798776759, ss3841788249, ss4437298747 NC_000001.11:3788456:T:C NC_000001.11:3788456:T:C (self)
ss12992562, ss19868035, ss20518462 NT_004321.15:1011794:T:C NC_000001.11:3788456:T:C (self)
ss44031829, ss97915439, ss105114903, ss138972028 NT_004350.19:3183652:T:C NC_000001.11:3788456:T:C (self)
107993, ss3892930599 NC_000001.10:3705020:T:G NC_000001.11:3788456:T:G (self)
1782334708 NC_000001.11:3788456:T:G NC_000001.11:3788456:T:G
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 rs9424282

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