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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs9578971

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr13:26166749 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.061600 (16305/264690, TOPMED)
G=0.061254 (8587/140186, GnomAD)
G=0.00067 (19/28258, 14KJPN) (+ 17 more)
G=0.05527 (1044/18890, ALFA)
G=0.00084 (14/16760, 8.3KJPN)
G=0.0503 (322/6404, 1000G_30x)
G=0.0489 (245/5008, 1000G)
G=0.0437 (196/4480, Estonian)
G=0.0379 (146/3854, ALSPAC)
G=0.0423 (157/3708, TWINSUK)
G=0.0017 (5/2922, KOREAN)
G=0.0016 (3/1832, Korea1K)
G=0.048 (48/998, GoNL)
G=0.043 (26/600, NorthernSweden)
G=0.056 (12/216, Qatari)
G=0.028 (6/216, Vietnamese)
A=0.44 (23/52, SGDP_PRJ)
G=0.05 (2/40, GENOME_DK)
A=0.5 (1/2, Siberian)
G=0.5 (1/2, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RNF6 : 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 18890 A=0.94473 G=0.05527
European Sub 14286 A=0.95450 G=0.04550
African Sub 2946 A=0.8938 G=0.1062
African Others Sub 114 A=0.842 G=0.158
African American Sub 2832 A=0.8958 G=0.1042
Asian Sub 112 A=0.991 G=0.009
East Asian Sub 86 A=0.99 G=0.01
Other Asian Sub 26 A=1.00 G=0.00
Latin American 1 Sub 146 A=0.938 G=0.062
Latin American 2 Sub 610 A=0.964 G=0.036
South Asian Sub 98 A=0.99 G=0.01
Other Sub 692 A=0.931 G=0.069


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 A=0.938400 G=0.061600
gnomAD - Genomes Global Study-wide 140186 A=0.938746 G=0.061254
gnomAD - Genomes European Sub 75928 A=0.95618 G=0.04382
gnomAD - Genomes African Sub 41998 A=0.89445 G=0.10555
gnomAD - Genomes American Sub 13654 A=0.96272 G=0.03728
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.9576 G=0.0424
gnomAD - Genomes East Asian Sub 3130 A=0.9837 G=0.0163
gnomAD - Genomes Other Sub 2152 A=0.9414 G=0.0586
14KJPN JAPANESE Study-wide 28258 A=0.99933 G=0.00067
Allele Frequency Aggregator Total Global 18890 A=0.94473 G=0.05527
Allele Frequency Aggregator European Sub 14286 A=0.95450 G=0.04550
Allele Frequency Aggregator African Sub 2946 A=0.8938 G=0.1062
Allele Frequency Aggregator Other Sub 692 A=0.931 G=0.069
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.964 G=0.036
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.938 G=0.062
Allele Frequency Aggregator Asian Sub 112 A=0.991 G=0.009
Allele Frequency Aggregator South Asian Sub 98 A=0.99 G=0.01
8.3KJPN JAPANESE Study-wide 16760 A=0.99916 G=0.00084
1000Genomes_30x Global Study-wide 6404 A=0.9497 G=0.0503
1000Genomes_30x African Sub 1786 A=0.8964 G=0.1036
1000Genomes_30x Europe Sub 1266 A=0.9463 G=0.0537
1000Genomes_30x South Asian Sub 1202 A=0.9892 G=0.0108
1000Genomes_30x East Asian Sub 1170 A=0.9761 G=0.0239
1000Genomes_30x American Sub 980 A=0.971 G=0.029
1000Genomes Global Study-wide 5008 A=0.9511 G=0.0489
1000Genomes African Sub 1322 A=0.8933 G=0.1067
1000Genomes East Asian Sub 1008 A=0.9782 G=0.0218
1000Genomes Europe Sub 1006 A=0.9503 G=0.0497
1000Genomes South Asian Sub 978 A=0.988 G=0.012
1000Genomes American Sub 694 A=0.971 G=0.029
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.9563 G=0.0437
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9621 G=0.0379
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9577 G=0.0423
KOREAN population from KRGDB KOREAN Study-wide 2922 A=0.9983 G=0.0017
Korean Genome Project KOREAN Study-wide 1832 A=0.9984 G=0.0016
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.952 G=0.048
Northern Sweden ACPOP Study-wide 600 A=0.957 G=0.043
Qatari Global Study-wide 216 A=0.944 G=0.056
A Vietnamese Genetic Variation Database Global Study-wide 216 A=0.972 G=0.028
SGDP_PRJ Global Study-wide 52 A=0.44 G=0.56
The Danish reference pan genome Danish Study-wide 40 A=0.95 G=0.05
Siberian Global Study-wide 2 A=0.5 G=0.5
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 13 NC_000013.11:g.26166749A>G
GRCh37.p13 chr 13 NC_000013.10:g.26740886A>G
RNF6 RefSeqGene NG_017042.2:g.60623T>C
Gene: RNF6, ring finger protein 6 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
RNF6 transcript variant 2 NM_183045.1:c.409-34298T>C N/A Intron Variant
RNF6 transcript variant 1 NM_005977.4:c. N/A Genic Downstream Transcript Variant
RNF6 transcript variant 4 NM_183043.3:c. N/A Genic Downstream Transcript Variant
RNF6 transcript variant 3 NM_183044.3:c. N/A Genic Downstream Transcript Variant
RNF6 transcript variant X13 XM_011535178.3:c.409-3429…

XM_011535178.3:c.409-34298T>C

 		N/A Intron Variant
RNF6 transcript variant X14 XM_047430498.1:c.409-3429…

XM_047430498.1:c.409-34298T>C

 		N/A Intron Variant
RNF6 transcript variant X15 XM_047430499.1:c.409-3429…

XM_047430499.1:c.409-34298T>C

 		N/A Intron Variant
RNF6 transcript variant X16 XM_047430500.1:c.409-3429…

XM_047430500.1:c.409-34298T>C

 		N/A Intron Variant
RNF6 transcript variant X1 XM_005266485.4:c. N/A Genic Downstream Transcript Variant
RNF6 transcript variant X3 XM_005266486.3:c. N/A Genic Downstream Transcript Variant
RNF6 transcript variant X2 XM_011535177.4:c. N/A Genic Downstream Transcript Variant
RNF6 transcript variant X6 XM_017020685.3:c. N/A Genic Downstream Transcript Variant
RNF6 transcript variant X7 XM_017020686.2:c. N/A Genic Downstream Transcript Variant
RNF6 transcript variant X12 XM_017020687.2:c. N/A Genic Downstream Transcript Variant
RNF6 transcript variant X4 XM_024449390.2:c. N/A Genic Downstream Transcript Variant
RNF6 transcript variant X9 XM_024449391.2:c. N/A Genic Downstream Transcript Variant
RNF6 transcript variant X11 XM_024449392.2:c. N/A Genic Downstream Transcript Variant
RNF6 transcript variant X5 XM_047430494.1:c. N/A Genic Downstream Transcript Variant
RNF6 transcript variant X8 XM_047430495.1:c. N/A Genic Downstream Transcript Variant
RNF6 transcript variant X10 XM_047430496.1:c. N/A Genic Downstream 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 A= G
GRCh38.p14 chr 13 NC_000013.11:g.26166749= NC_000013.11:g.26166749A>G
GRCh37.p13 chr 13 NC_000013.10:g.26740886= NC_000013.10:g.26740886A>G
RNF6 RefSeqGene NG_017042.2:g.60623= NG_017042.2:g.60623T>C
RNF6 transcript variant 2 NM_183045.1:c.409-34298= NM_183045.1:c.409-34298T>C
RNF6 transcript variant X13 XM_011535178.3:c.409-34298= XM_011535178.3:c.409-34298T>C
RNF6 transcript variant X14 XM_047430498.1:c.409-34298= XM_047430498.1:c.409-34298T>C
RNF6 transcript variant X15 XM_047430499.1:c.409-34298= XM_047430499.1:c.409-34298T>C
RNF6 transcript variant X16 XM_047430500.1:c.409-34298= XM_047430500.1:c.409-34298T>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#.

48 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss13304097 Dec 05, 2003 (119)
2 HGSV ss79754527 Dec 14, 2007 (130)
3 BUSHMAN ss198990550 Jul 04, 2010 (132)
4 1000GENOMES ss226088175 Jul 14, 2010 (132)
5 1000GENOMES ss236182251 Jul 15, 2010 (132)
6 PJP ss291560587 May 09, 2011 (134)
7 TISHKOFF ss563559208 Apr 25, 2013 (138)
8 SSMP ss659154631 Apr 25, 2013 (138)
9 EVA-GONL ss990207947 Aug 21, 2014 (142)
10 JMKIDD_LAB ss1078948440 Aug 21, 2014 (142)
11 1000GENOMES ss1347547162 Aug 21, 2014 (142)
12 EVA_GENOME_DK ss1576681838 Apr 01, 2015 (144)
13 EVA_UK10K_ALSPAC ss1629917119 Apr 01, 2015 (144)
14 EVA_DECODE ss1642312746 Apr 01, 2015 (144)
15 EVA_UK10K_TWINSUK ss1672911152 Apr 01, 2015 (144)
16 HAMMER_LAB ss1807532249 Sep 08, 2015 (146)
17 WEILL_CORNELL_DGM ss1933576750 Feb 12, 2016 (147)
18 JJLAB ss2027543359 Sep 14, 2016 (149)
19 USC_VALOUEV ss2155907496 Dec 20, 2016 (150)
20 HUMAN_LONGEVITY ss2194953190 Dec 20, 2016 (150)
21 GNOMAD ss2917743268 Nov 08, 2017 (151)
22 SWEGEN ss3010743686 Nov 08, 2017 (151)
23 CSHL ss3350372312 Nov 08, 2017 (151)
24 EGCUT_WGS ss3678004779 Jul 13, 2019 (153)
25 EVA_DECODE ss3694953309 Jul 13, 2019 (153)
26 ACPOP ss3739595104 Jul 13, 2019 (153)
27 EVA ss3751252661 Jul 13, 2019 (153)
28 KHV_HUMAN_GENOMES ss3816583916 Jul 13, 2019 (153)
29 EVA ss3833456119 Apr 27, 2020 (154)
30 EVA ss3840304450 Apr 27, 2020 (154)
31 EVA ss3845789039 Apr 27, 2020 (154)
32 SGDP_PRJ ss3879622031 Apr 27, 2020 (154)
33 KRGDB ss3928441253 Apr 27, 2020 (154)
34 KOGIC ss3973232198 Apr 27, 2020 (154)
35 TOPMED ss4940382943 Apr 26, 2021 (155)
36 TOMMO_GENOMICS ss5209236706 Apr 26, 2021 (155)
37 1000G_HIGH_COVERAGE ss5293143934 Oct 16, 2022 (156)
38 EVA ss5409690213 Oct 16, 2022 (156)
39 HUGCELL_USP ss5487565104 Oct 16, 2022 (156)
40 EVA ss5510912833 Oct 16, 2022 (156)
41 1000G_HIGH_COVERAGE ss5591799592 Oct 16, 2022 (156)
42 SANFORD_IMAGENETICS ss5654429315 Oct 16, 2022 (156)
43 TOMMO_GENOMICS ss5760894471 Oct 16, 2022 (156)
44 YY_MCH ss5813962801 Oct 16, 2022 (156)
45 EVA ss5839240840 Oct 16, 2022 (156)
46 EVA ss5850654003 Oct 16, 2022 (156)
47 EVA ss5924422822 Oct 16, 2022 (156)
48 EVA ss5945833869 Oct 16, 2022 (156)
49 1000Genomes NC_000013.10 - 26740886 Oct 12, 2018 (152)
50 1000Genomes_30x NC_000013.11 - 26166749 Oct 16, 2022 (156)
51 The Avon Longitudinal Study of Parents and Children NC_000013.10 - 26740886 Oct 12, 2018 (152)
52 Genetic variation in the Estonian population NC_000013.10 - 26740886 Oct 12, 2018 (152)
53 The Danish reference pan genome NC_000013.10 - 26740886 Apr 27, 2020 (154)
54 gnomAD - Genomes NC_000013.11 - 26166749 Apr 26, 2021 (155)
55 Genome of the Netherlands Release 5 NC_000013.10 - 26740886 Apr 27, 2020 (154)
56 KOREAN population from KRGDB NC_000013.10 - 26740886 Apr 27, 2020 (154)
57 Korean Genome Project NC_000013.11 - 26166749 Apr 27, 2020 (154)
58 Northern Sweden NC_000013.10 - 26740886 Jul 13, 2019 (153)
59 Qatari NC_000013.10 - 26740886 Apr 27, 2020 (154)
60 SGDP_PRJ NC_000013.10 - 26740886 Apr 27, 2020 (154)
61 Siberian NC_000013.10 - 26740886 Apr 27, 2020 (154)
62 8.3KJPN NC_000013.10 - 26740886 Apr 26, 2021 (155)
63 14KJPN NC_000013.11 - 26166749 Oct 16, 2022 (156)
64 TopMed NC_000013.11 - 26166749 Apr 26, 2021 (155)
65 UK 10K study - Twins NC_000013.10 - 26740886 Oct 12, 2018 (152)
66 A Vietnamese Genetic Variation Database NC_000013.10 - 26740886 Jul 13, 2019 (153)
67 ALFA NC_000013.11 - 26166749 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).

Associated ID History Updated (Build)
rs57043736 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss79754527, ss198990550, ss291560587, ss1642312746 NC_000013.9:25638885:A:G NC_000013.11:26166748:A:G (self)
60392684, 33539525, 23743027, 3225989, 14965011, 35618647, 12879969, 15618680, 31639011, 8423850, 67206013, 33539525, 7440224, ss226088175, ss236182251, ss563559208, ss659154631, ss990207947, ss1078948440, ss1347547162, ss1576681838, ss1629917119, ss1672911152, ss1807532249, ss1933576750, ss2027543359, ss2155907496, ss2917743268, ss3010743686, ss3350372312, ss3678004779, ss3739595104, ss3751252661, ss3833456119, ss3840304450, ss3879622031, ss3928441253, ss5209236706, ss5409690213, ss5510912833, ss5654429315, ss5839240840, ss5945833869 NC_000013.10:26740885:A:G NC_000013.11:26166748:A:G (self)
79325527, 425871657, 29610199, 94731575, 155928601, 6263547035, ss2194953190, ss3694953309, ss3816583916, ss3845789039, ss3973232198, ss4940382943, ss5293143934, ss5487565104, ss5591799592, ss5760894471, ss5813962801, ss5850654003, ss5924422822 NC_000013.11:26166748:A:G NC_000013.11:26166748:A:G (self)
ss13304097 NT_009799.12:7720885:A:G NC_000013.11:26166748:A: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 rs9578971

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