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.

rs9424285

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3793615 (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 / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.114564 (30324/264690, TOPMED)
A=0.100727 (14114/140122, GnomAD)
A=0.10429 (1970/18890, ALFA) (+ 15 more)
A=0.40370 (6766/16760, 8.3KJPN)
A=0.2232 (1118/5008, 1000G)
A=0.1259 (564/4480, Estonian)
A=0.0898 (346/3854, ALSPAC)
A=0.0782 (290/3708, TWINSUK)
G=0.4949 (1450/2930, KOREAN)
G=0.4749 (870/1832, Korea1K)
A=0.078 (78/998, GoNL)
A=0.107 (64/600, NorthernSweden)
A=0.151 (47/312, HapMap)
A=0.139 (30/216, Qatari)
G=0.347 (75/216, SGDP_PRJ)
G=0.472 (100/212, Vietnamese)
A=0.12 (5/40, GENOME_DK)
G=0.41 (13/32, 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.3793615G>A
GRCh38.p13 chr 1 NC_000001.11:g.3793615G>C
GRCh37.p13 chr 1 NC_000001.10:g.3710179G>A
GRCh37.p13 chr 1 NC_000001.10:g.3710179G>C
Gene: LRRC47, leucine rich repeat containing 47 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LRRC47 transcript NM_020710.3:c.615+2247C>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 18890 G=0.89571 A=0.10429
European Sub 14286 G=0.89878 A=0.10122
African Sub 2946 G=0.9345 A=0.0655
African Others Sub 114 G=0.974 A=0.026
African American Sub 2832 G=0.9329 A=0.0671
Asian Sub 112 G=0.589 A=0.411
East Asian Sub 86 G=0.58 A=0.42
Other Asian Sub 26 G=0.62 A=0.38
Latin American 1 Sub 146 G=0.870 A=0.130
Latin American 2 Sub 610 G=0.775 A=0.225
South Asian Sub 98 G=0.56 A=0.44
Other Sub 692 G=0.876 A=0.124


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=0.885436 A=0.114564
gnomAD - Genomes Global Study-wide 140122 G=0.899273 A=0.100727
gnomAD - Genomes European Sub 75890 G=0.90684 A=0.09316
gnomAD - Genomes African Sub 42002 G=0.93272 A=0.06728
gnomAD - Genomes American Sub 13636 G=0.85326 A=0.14674
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.8947 A=0.1053
gnomAD - Genomes East Asian Sub 3120 G=0.4792 A=0.5208
gnomAD - Genomes Other Sub 2150 G=0.8874 A=0.1126
Allele Frequency Aggregator Total Global 18890 G=0.89571 A=0.10429
Allele Frequency Aggregator European Sub 14286 G=0.89878 A=0.10122
Allele Frequency Aggregator African Sub 2946 G=0.9345 A=0.0655
Allele Frequency Aggregator Other Sub 692 G=0.876 A=0.124
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.775 A=0.225
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.870 A=0.130
Allele Frequency Aggregator Asian Sub 112 G=0.589 A=0.411
Allele Frequency Aggregator South Asian Sub 98 G=0.56 A=0.44
8.3KJPN JAPANESE Study-wide 16760 G=0.59630 A=0.40370
1000Genomes Global Study-wide 5008 G=0.7768 A=0.2232
1000Genomes African Sub 1322 G=0.9561 A=0.0439
1000Genomes East Asian Sub 1008 G=0.4762 A=0.5238
1000Genomes Europe Sub 1006 G=0.9105 A=0.0895
1000Genomes South Asian Sub 978 G=0.655 A=0.345
1000Genomes American Sub 694 G=0.849 A=0.151
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.8741 A=0.1259
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9102 A=0.0898
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9218 A=0.0782
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.4949 A=0.5051, C=0.0000
Korean Genome Project KOREAN Study-wide 1832 G=0.4749 A=0.5251
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.922 A=0.078
Northern Sweden ACPOP Study-wide 600 G=0.893 A=0.107
HapMap Global Study-wide 312 G=0.849 A=0.151
HapMap African Sub 116 G=0.966 A=0.034
HapMap American Sub 116 G=0.922 A=0.078
HapMap Asian Sub 80 G=0.57 A=0.42
Qatari Global Study-wide 216 G=0.861 A=0.139
SGDP_PRJ Global Study-wide 216 G=0.347 A=0.653
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.472 A=0.528
The Danish reference pan genome Danish Study-wide 40 G=0.88 A=0.12
Siberian Global Study-wide 32 G=0.41 A=0.59
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 C
GRCh38.p13 chr 1 NC_000001.11:g.3793615= NC_000001.11:g.3793615G>A NC_000001.11:g.3793615G>C
GRCh37.p13 chr 1 NC_000001.10:g.3710179= NC_000001.10:g.3710179G>A NC_000001.10:g.3710179G>C
LRRC47 transcript NM_020710.2:c.615+2247= NM_020710.2:c.615+2247C>T NM_020710.2:c.615+2247C>G
LRRC47 transcript NM_020710.3:c.615+2247= NM_020710.3:c.615+2247C>T NM_020710.3:c.615+2247C>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#.

49 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss12992565 Dec 05, 2003 (119)
2 CSHL-HAPMAP ss19835524 Feb 27, 2004 (120)
3 ABI ss41278502 Mar 15, 2006 (126)
4 BGI ss105114909 Dec 01, 2009 (131)
5 ENSEMBL ss161249341 Dec 01, 2009 (131)
6 COMPLETE_GENOMICS ss163737611 Jul 04, 2010 (132)
7 BCM-HGSC-SUB ss205411550 Jul 04, 2010 (132)
8 1000GENOMES ss218203202 Jul 14, 2010 (132)
9 1000GENOMES ss230404082 Jul 14, 2010 (132)
10 1000GENOMES ss238122981 Jul 15, 2010 (132)
11 GMI ss275691390 May 04, 2012 (137)
12 GMI ss283990985 Apr 25, 2013 (138)
13 TISHKOFF ss553734577 Apr 25, 2013 (138)
14 SSMP ss647536332 Apr 25, 2013 (138)
15 EVA-GONL ss974796261 Aug 21, 2014 (142)
16 JMKIDD_LAB ss1067627182 Aug 21, 2014 (142)
17 1000GENOMES ss1289451046 Aug 21, 2014 (142)
18 EVA_GENOME_DK ss1573860053 Apr 01, 2015 (144)
19 EVA_DECODE ss1584155053 Apr 01, 2015 (144)
20 EVA_UK10K_ALSPAC ss1599427042 Apr 01, 2015 (144)
21 EVA_UK10K_TWINSUK ss1642421075 Apr 01, 2015 (144)
22 WEILL_CORNELL_DGM ss1917991807 Feb 12, 2016 (147)
23 GENOMED ss1966671330 Jul 19, 2016 (147)
24 JJLAB ss2019512021 Sep 14, 2016 (149)
25 USC_VALOUEV ss2147502414 Dec 20, 2016 (150)
26 HUMAN_LONGEVITY ss2159573328 Dec 20, 2016 (150)
27 TOPMED ss2321728269 Dec 20, 2016 (150)
28 SYSTEMSBIOZJU ss2624271769 Nov 08, 2017 (151)
29 GRF ss2697396436 Nov 08, 2017 (151)
30 GNOMAD ss2750970522 Nov 08, 2017 (151)
31 SWEGEN ss2986201051 Nov 08, 2017 (151)
32 BIOINF_KMB_FNS_UNIBA ss3023519637 Nov 08, 2017 (151)
33 TOPMED ss3067122661 Nov 08, 2017 (151)
34 CSHL ss3343288845 Nov 08, 2017 (151)
35 EGCUT_WGS ss3654302229 Jul 12, 2019 (153)
36 EVA_DECODE ss3686046887 Jul 12, 2019 (153)
37 ACPOP ss3726739866 Jul 12, 2019 (153)
38 EVA ss3745755089 Jul 12, 2019 (153)
39 PACBIO ss3783308711 Jul 12, 2019 (153)
40 PACBIO ss3788985599 Jul 12, 2019 (153)
41 PACBIO ss3793858227 Jul 12, 2019 (153)
42 KHV_HUMAN_GENOMES ss3798776817 Jul 12, 2019 (153)
43 EVA ss3836384098 Apr 25, 2020 (154)
44 EVA ss3841788261 Apr 25, 2020 (154)
45 SGDP_PRJ ss3848069189 Apr 25, 2020 (154)
46 KRGDB ss3892930700 Apr 25, 2020 (154)
47 KOGIC ss3943692513 Apr 25, 2020 (154)
48 TOPMED ss4437300285 Apr 25, 2021 (155)
49 TOMMO_GENOMICS ss5142200996 Apr 25, 2021 (155)
50 1000Genomes NC_000001.10 - 3710179 Oct 11, 2018 (152)
51 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 3710179 Oct 11, 2018 (152)
52 Genetic variation in the Estonian population NC_000001.10 - 3710179 Oct 11, 2018 (152)
53 The Danish reference pan genome NC_000001.10 - 3710179 Apr 25, 2020 (154)
54 gnomAD - Genomes NC_000001.11 - 3793615 Apr 25, 2021 (155)
55 Genome of the Netherlands Release 5 NC_000001.10 - 3710179 Apr 25, 2020 (154)
56 HapMap NC_000001.11 - 3793615 Apr 25, 2020 (154)
57 KOREAN population from KRGDB NC_000001.10 - 3710179 Apr 25, 2020 (154)
58 Korean Genome Project NC_000001.11 - 3793615 Apr 25, 2020 (154)
59 Northern Sweden NC_000001.10 - 3710179 Jul 12, 2019 (153)
60 Qatari NC_000001.10 - 3710179 Apr 25, 2020 (154)
61 SGDP_PRJ NC_000001.10 - 3710179 Apr 25, 2020 (154)
62 Siberian NC_000001.10 - 3710179 Apr 25, 2020 (154)
63 8.3KJPN NC_000001.10 - 3710179 Apr 25, 2021 (155)
64 TopMed NC_000001.11 - 3793615 Apr 25, 2021 (155)
65 UK 10K study - Twins NC_000001.10 - 3710179 Oct 11, 2018 (152)
66 A Vietnamese Genetic Variation Database NC_000001.10 - 3710179 Jul 12, 2019 (153)
67 ALFA NC_000001.11 - 3793615 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
ss163737611, ss205411550, ss275691390, ss283990985, ss1584155053 NC_000001.9:3700038:G:A NC_000001.11:3793614:G:A (self)
119055, 53252, 40477, 1367287, 22888, 108094, 24731, 33737, 86169, 18768, 170303, 53252, 11239, ss218203202, ss230404082, ss238122981, ss553734577, ss647536332, ss974796261, ss1067627182, ss1289451046, ss1573860053, ss1599427042, ss1642421075, ss1917991807, ss1966671330, ss2019512021, ss2147502414, ss2321728269, ss2624271769, ss2697396436, ss2750970522, ss2986201051, ss3343288845, ss3654302229, ss3726739866, ss3745755089, ss3783308711, ss3788985599, ss3793858227, ss3836384098, ss3848069189, ss3892930700, ss5142200996 NC_000001.10:3710178:G:A NC_000001.11:3793614:G:A (self)
859094, 2784, 70514, 564343, 906620, 747342027, ss2159573328, ss3023519637, ss3067122661, ss3686046887, ss3798776817, ss3841788261, ss3943692513, ss4437300285 NC_000001.11:3793614:G:A NC_000001.11:3793614:G:A (self)
ss12992565, ss19835524 NT_004321.15:1016952:G:A NC_000001.11:3793614:G:A (self)
ss41278502, ss105114909, ss161249341 NT_004350.19:3188810:G:A NC_000001.11:3793614:G:A (self)
108094, ss3892930700 NC_000001.10:3710178:G:C NC_000001.11:3793614:G: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 rs9424285

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