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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.

rs471068

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr9:5337913 (GRCh38.p14) 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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000008 (2/264690, TOPMED)
G=0.000800 (112/140074, GnomAD)
G=0.00037 (7/18874, ALFA) (+ 5 more)
G=0.00185 (31/16760, 8.3KJPN)
G=0.0008 (5/6404, 1000G_30x)
G=0.0016 (8/5008, 1000G)
G=0.0014 (4/2920, KOREAN)
G=0.0005 (1/1832, Korea1K)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RLN2 : Intron Variant
RLN1 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome

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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 18874 T=0.99963 A=0.00000, G=0.00037
European Sub 14274 T=0.99951 A=0.00000, G=0.00049
African Sub 2946 T=1.0000 A=0.0000, G=0.0000
African Others Sub 114 T=1.000 A=0.000, G=0.000
African American Sub 2832 T=1.0000 A=0.0000, G=0.0000
Asian Sub 112 T=1.000 A=0.000, G=0.000
East Asian Sub 86 T=1.00 A=0.00, G=0.00
Other Asian Sub 26 T=1.00 A=0.00, G=0.00
Latin American 1 Sub 146 T=1.000 A=0.000, G=0.000
Latin American 2 Sub 608 T=1.000 A=0.000, G=0.000
South Asian Sub 98 T=1.00 A=0.00, G=0.00
Other Sub 690 T=1.000 A=0.000, 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=0.999992 A=0.000008
gnomAD - Genomes Global Study-wide 140074 T=0.999200 G=0.000800
gnomAD - Genomes European Sub 75868 T=0.99918 G=0.00082
gnomAD - Genomes African Sub 41970 T=0.99957 G=0.00043
gnomAD - Genomes American Sub 13638 T=0.99978 G=0.00022
gnomAD - Genomes Ashkenazi Jewish Sub 3318 T=0.9934 G=0.0066
gnomAD - Genomes East Asian Sub 3130 T=0.9981 G=0.0019
gnomAD - Genomes Other Sub 2150 T=0.9995 G=0.0005
Allele Frequency Aggregator Total Global 18874 T=0.99963 A=0.00000, G=0.00037
Allele Frequency Aggregator European Sub 14274 T=0.99951 A=0.00000, G=0.00049
Allele Frequency Aggregator African Sub 2946 T=1.0000 A=0.0000, G=0.0000
Allele Frequency Aggregator Other Sub 690 T=1.000 A=0.000, G=0.000
Allele Frequency Aggregator Latin American 2 Sub 608 T=1.000 A=0.000, G=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 T=1.000 A=0.000, G=0.000
Allele Frequency Aggregator Asian Sub 112 T=1.000 A=0.000, G=0.000
Allele Frequency Aggregator South Asian Sub 98 T=1.00 A=0.00, G=0.00
8.3KJPN JAPANESE Study-wide 16760 T=0.99815 G=0.00185
1000Genomes_30x Global Study-wide 6404 T=0.9992 G=0.0008
1000Genomes_30x African Sub 1786 T=0.9983 G=0.0017
1000Genomes_30x Europe Sub 1266 T=0.9992 G=0.0008
1000Genomes_30x South Asian Sub 1202 T=1.0000 G=0.0000
1000Genomes_30x East Asian Sub 1170 T=0.9991 G=0.0009
1000Genomes_30x American Sub 980 T=1.000 G=0.000
1000Genomes Global Study-wide 5008 T=0.9984 G=0.0016
1000Genomes African Sub 1322 T=0.9947 G=0.0053
1000Genomes East Asian Sub 1008 T=1.0000 G=0.0000
1000Genomes Europe Sub 1006 T=0.9990 G=0.0010
1000Genomes South Asian Sub 978 T=1.000 G=0.000
1000Genomes American Sub 694 T=1.000 G=0.000
KOREAN population from KRGDB KOREAN Study-wide 2920 T=0.9986 G=0.0014
Korean Genome Project KOREAN Study-wide 1832 T=0.9995 G=0.0005
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.p14 chr 9 NC_000009.12:g.5337913T>A
GRCh38.p14 chr 9 NC_000009.12:g.5337913T>G
GRCh37.p13 chr 9 NC_000009.11:g.5337913T>A
GRCh37.p13 chr 9 NC_000009.11:g.5337913T>G
Gene: RLN1, relaxin 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
RLN1 transcript NM_006911.4:c.211+1623A>T N/A Intron Variant
RLN1 transcript variant X1 XM_047423703.1:c.312+1349…

XM_047423703.1:c.312+1349A>T

N/A Intron Variant
RLN1 transcript variant X2 XM_047423704.1:c.-48+1349…

XM_047423704.1:c.-48+1349A>T

N/A Intron Variant
RLN1 transcript variant X3 XM_047423705.1:c.-48+1450…

XM_047423705.1:c.-48+1450A>T

N/A Intron Variant
RLN1 transcript variant X4 XM_047423706.1:c.-47-2316…

XM_047423706.1:c.-47-2316A>T

N/A Intron Variant
Gene: RLN2, relaxin 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
RLN2 transcript variant 3 NM_001329191.2:c. N/A Genic Upstream Transcript Variant
RLN2 transcript variant 2 NM_005059.4:c. N/A Genic Upstream Transcript Variant
RLN2 transcript variant 1 NM_134441.3:c. N/A Genic Upstream Transcript Variant
RLN2 transcript variant X1 XM_047423707.1:c.-338+134…

XM_047423707.1:c.-338+1349A>T

N/A Intron Variant
RLN2 transcript variant X3 XM_047423709.1:c.-2641+13…

XM_047423709.1:c.-2641+1349A>T

N/A Intron Variant
RLN2 transcript variant X2 XM_047423708.1:c. N/A Genic Upstream Transcript 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
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 G
GRCh38.p14 chr 9 NC_000009.12:g.5337913= NC_000009.12:g.5337913T>A NC_000009.12:g.5337913T>G
GRCh37.p13 chr 9 NC_000009.11:g.5337913= NC_000009.11:g.5337913T>A NC_000009.11:g.5337913T>G
RLN1 transcript NM_006911.3:c.211+1623= NM_006911.3:c.211+1623A>T NM_006911.3:c.211+1623A>C
RLN1 transcript NM_006911.4:c.211+1623= NM_006911.4:c.211+1623A>T NM_006911.4:c.211+1623A>C
RLN1 transcript variant X1 XM_005251541.1:c.312+1349= XM_005251541.1:c.312+1349A>T XM_005251541.1:c.312+1349A>C
RLN1 transcript variant X1 XM_047423703.1:c.312+1349= XM_047423703.1:c.312+1349A>T XM_047423703.1:c.312+1349A>C
RLN1 transcript variant X2 XM_047423704.1:c.-48+1349= XM_047423704.1:c.-48+1349A>T XM_047423704.1:c.-48+1349A>C
RLN1 transcript variant X3 XM_047423705.1:c.-48+1450= XM_047423705.1:c.-48+1450A>T XM_047423705.1:c.-48+1450A>C
RLN1 transcript variant X4 XM_047423706.1:c.-47-2316= XM_047423706.1:c.-47-2316A>T XM_047423706.1:c.-47-2316A>C
RLN2 transcript variant X1 XM_047423707.1:c.-338+1349= XM_047423707.1:c.-338+1349A>T XM_047423707.1:c.-338+1349A>C
RLN2 transcript variant X3 XM_047423709.1:c.-2641+1349= XM_047423709.1:c.-2641+1349A>T XM_047423709.1:c.-2641+1349A>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#.

17 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss640410 Aug 11, 2000 (83)
2 TSC-CSHL ss2725731 Jan 22, 2001 (92)
3 TSC-CSHL ss5196943 Oct 08, 2002 (108)
4 1000GENOMES ss1332682732 Aug 21, 2014 (142)
5 GNOMAD ss2874819871 Nov 08, 2017 (151)
6 SWEGEN ss3004301552 Nov 08, 2017 (151)
7 EVA ss3768848398 Jul 13, 2019 (153)
8 KRGDB ss3919042049 Apr 26, 2020 (154)
9 KOGIC ss3965205724 Apr 26, 2020 (154)
10 TOPMED ss4810641699 Apr 26, 2021 (155)
11 TOMMO_GENOMICS ss5191844909 Apr 26, 2021 (155)
12 1000G_HIGH_COVERAGE ss5279610917 Oct 16, 2022 (156)
13 EVA ss5385698681 Oct 16, 2022 (156)
14 1000G_HIGH_COVERAGE ss5571273730 Oct 16, 2022 (156)
15 TOMMO_GENOMICS ss5734827721 Oct 16, 2022 (156)
16 TOMMO_GENOMICS ss5734827722 Oct 16, 2022 (156)
17 EVA ss5915310955 Oct 16, 2022 (156)
18 1000Genomes NC_000009.11 - 5337913 Oct 12, 2018 (152)
19 1000Genomes_30x NC_000009.12 - 5337913 Oct 16, 2022 (156)
20 gnomAD - Genomes NC_000009.12 - 5337913 Apr 26, 2021 (155)
21 KOREAN population from KRGDB NC_000009.11 - 5337913 Apr 26, 2020 (154)
22 Korean Genome Project NC_000009.12 - 5337913 Apr 26, 2020 (154)
23 8.3KJPN NC_000009.11 - 5337913 Apr 26, 2021 (155)
24 14KJPN

Submission ignored due to conflicting rows:
Row 68664825 (NC_000009.12:5337912:T:G 42/28256)
Row 68664826 (NC_000009.12:5337912:T:A 1/28256)

- Oct 16, 2022 (156)
25 14KJPN

Submission ignored due to conflicting rows:
Row 68664825 (NC_000009.12:5337912:T:G 42/28256)
Row 68664826 (NC_000009.12:5337912:T:A 1/28256)

- Oct 16, 2022 (156)
26 TopMed NC_000009.12 - 5337913 Apr 26, 2021 (155)
27 ALFA NC_000009.12 - 5337913 Apr 26, 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
648019260, 10823087170, ss4810641699, ss5734827722 NC_000009.12:5337912:T:A NC_000009.12:5337912:T:A (self)
44904891, 26219443, 49814216, ss1332682732, ss2874819871, ss3004301552, ss3768848398, ss3919042049, ss5191844909, ss5385698681 NC_000009.11:5337912:T:G NC_000009.12:5337912:T:G (self)
58799665, 316540936, 21583725, 10823087170, ss3965205724, ss5279610917, ss5571273730, ss5734827721, ss5915310955 NC_000009.12:5337912:T:G NC_000009.12:5337912:T:G (self)
ss640410, ss2725731, ss5196943 NT_008413.18:5327912:T:G NC_000009.12:5337912:T: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 rs471068

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.post761+d5e8e07