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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.

rs35794454

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:43533927 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000212 (56/264690, TOPMED)
A=0.000088 (22/249182, GnomAD_exome)
A=0.000114 (21/184984, ALFA) (+ 6 more)
A=0.000185 (26/140176, GnomAD)
A=0.000083 (10/120524, ExAC)
A=0.00034 (27/78698, PAGE_STUDY)
A=0.00025 (3/11816, GO-ESP)
A=0.001 (1/792, PRJEB37584)
A=0.005 (1/216, Qatari)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
XPO5 : Missense Variant
POLR1C : Intron Variant
Publications
1 citation
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 201396 G=0.999886 A=0.000114
European Sub 167752 G=0.999905 A=0.000095
African Sub 10286 G=0.99942 A=0.00058
African Others Sub 382 G=1.000 A=0.000
African American Sub 9904 G=0.9994 A=0.0006
Asian Sub 6298 G=1.0000 A=0.0000
East Asian Sub 4478 G=1.0000 A=0.0000
Other Asian Sub 1820 G=1.0000 A=0.0000
Latin American 1 Sub 804 G=1.000 A=0.000
Latin American 2 Sub 974 G=1.000 A=0.000
South Asian Sub 280 G=1.000 A=0.000
Other Sub 15002 G=0.99993 A=0.00007


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=0.999788 A=0.000212
gnomAD - Exomes Global Study-wide 249182 G=0.999912 A=0.000088
gnomAD - Exomes European Sub 134520 G=0.999926 A=0.000074
gnomAD - Exomes Asian Sub 48574 G=0.99996 A=0.00004
gnomAD - Exomes American Sub 34496 G=0.99986 A=0.00014
gnomAD - Exomes African Sub 15476 G=0.99974 A=0.00026
gnomAD - Exomes Ashkenazi Jewish Sub 10064 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6052 G=0.9998 A=0.0002
Allele Frequency Aggregator Total Global 184984 G=0.999886 A=0.000114
Allele Frequency Aggregator European Sub 157612 G=0.999905 A=0.000095
Allele Frequency Aggregator Other Sub 13568 G=0.99993 A=0.00007
Allele Frequency Aggregator Asian Sub 6298 G=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 5448 G=0.9991 A=0.0009
Allele Frequency Aggregator Latin American 2 Sub 974 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 804 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 280 G=1.000 A=0.000
gnomAD - Genomes Global Study-wide 140176 G=0.999815 A=0.000185
gnomAD - Genomes European Sub 75904 G=0.99993 A=0.00007
gnomAD - Genomes African Sub 42022 G=0.99950 A=0.00050
gnomAD - Genomes American Sub 13646 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3130 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2150 G=1.0000 A=0.0000
ExAC Global Study-wide 120524 G=0.999917 A=0.000083
ExAC Europe Sub 73244 G=0.99990 A=0.00010
ExAC Asian Sub 25108 G=0.99996 A=0.00004
ExAC American Sub 11552 G=1.00000 A=0.00000
ExAC African Sub 9724 G=0.9998 A=0.0002
ExAC Other Sub 896 G=1.000 A=0.000
The PAGE Study Global Study-wide 78698 G=0.99966 A=0.00034
The PAGE Study AfricanAmerican Sub 32512 G=0.99932 A=0.00068
The PAGE Study Mexican Sub 10810 G=0.99981 A=0.00019
The PAGE Study Asian Sub 8318 G=0.9999 A=0.0001
The PAGE Study PuertoRican Sub 7918 G=1.0000 A=0.0000
The PAGE Study NativeHawaiian Sub 4534 G=1.0000 A=0.0000
The PAGE Study Cuban Sub 4230 G=1.0000 A=0.0000
The PAGE Study Dominican Sub 3828 G=0.9997 A=0.0003
The PAGE Study CentralAmerican Sub 2450 G=1.0000 A=0.0000
The PAGE Study SouthAmerican Sub 1982 G=0.9995 A=0.0005
The PAGE Study NativeAmerican Sub 1260 G=1.0000 A=0.0000
The PAGE Study SouthAsian Sub 856 G=1.000 A=0.000
GO Exome Sequencing Project Global Study-wide 11816 G=0.99975 A=0.00025
GO Exome Sequencing Project European American Sub 8156 G=0.9999 A=0.0001
GO Exome Sequencing Project African American Sub 3660 G=0.9995 A=0.0005
CNV burdens in cranial meningiomas Global Study-wide 792 G=0.999 A=0.001
CNV burdens in cranial meningiomas CRM Sub 792 G=0.999 A=0.001
Qatari Global Study-wide 216 G=0.995 A=0.005
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 6 NC_000006.12:g.43533927G>A
GRCh37.p13 chr 6 NC_000006.11:g.43501664G>A
POLR1C RefSeqGene NG_028283.3:g.29226G>A
XPO5 RefSeqGene NG_051658.1:g.47149C>T
Gene: POLR1C, RNA polymerase I and III subunit C (plus strand)
Molecule type Change Amino acid[Codon] SO Term
POLR1C transcript variant 2 NM_001318876.2:c.945+4656…

NM_001318876.2:c.945+4656G>A

 		N/A Intron Variant
POLR1C transcript variant 3 NM_001363658.2:c.922+1287…

NM_001363658.2:c.922+12879G>A

 		N/A Intron Variant
POLR1C transcript variant 1 NM_203290.4:c. N/A Genic Downstream Transcript Variant
POLR1C transcript variant X1 XM_047419577.1:c.*4572= N/A 3 Prime UTR Variant
Gene: XPO5, exportin 5 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
XPO5 transcript variant 1 NM_020750.3:c.2423C>T A [GCG] > V [GTG] Coding Sequence Variant
exportin-5 NP_065801.1:p.Ala808Val A (Ala) > V (Val) Missense Variant
XPO5 transcript variant 2 NR_144392.2:n.2735C>T N/A Non Coding 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 G= A
GRCh38.p14 chr 6 NC_000006.12:g.43533927= NC_000006.12:g.43533927G>A
GRCh37.p13 chr 6 NC_000006.11:g.43501664= NC_000006.11:g.43501664G>A
POLR1C RefSeqGene NG_028283.3:g.29226= NG_028283.3:g.29226G>A
XPO5 RefSeqGene NG_051658.1:g.47149= NG_051658.1:g.47149C>T
XPO5 transcript variant 1 NM_020750.3:c.2423= NM_020750.3:c.2423C>T
XPO5 transcript variant 1 NM_020750.2:c.2423= NM_020750.2:c.2423C>T
XPO5 transcript variant 2 NR_144392.2:n.2735= NR_144392.2:n.2735C>T
XPO5 transcript variant 2 NR_144392.1:n.2772= NR_144392.1:n.2772C>T
POLR1C transcript variant X1 XM_047419577.1:c.*4572= XM_047419577.1:c.*4572G>A
exportin-5 NP_065801.1:p.Ala808= NP_065801.1:p.Ala808Val
POLR1C transcript variant 2 NM_001318876.2:c.945+4656= NM_001318876.2:c.945+4656G>A
POLR1C transcript variant 3 NM_001363658.2:c.922+12879= NM_001363658.2:c.922+12879G>A
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#.

42 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 APPLERA_GI ss48417284 Mar 15, 2006 (126)
2 ILLUMINA ss74998094 Dec 07, 2007 (129)
3 KRIBB_YJKIM ss119918859 Dec 01, 2009 (131)
4 ILLUMINA ss173605095 Jul 04, 2010 (132)
5 EXOME_CHIP ss491386391 May 04, 2012 (137)
6 ILLUMINA ss537181077 Sep 08, 2015 (146)
7 NHLBI-ESP ss712712187 Apr 25, 2013 (138)
8 ILLUMINA ss780849732 Sep 08, 2015 (146)
9 ILLUMINA ss783533545 Sep 08, 2015 (146)
10 EVA_EXAC ss1688335311 Apr 01, 2015 (144)
11 ILLUMINA ss1752638031 Sep 08, 2015 (146)
12 ILLUMINA ss1917805935 Feb 12, 2016 (147)
13 WEILL_CORNELL_DGM ss1926130635 Feb 12, 2016 (147)
14 ILLUMINA ss1946178590 Feb 12, 2016 (147)
15 ILLUMINA ss1958906122 Feb 12, 2016 (147)
16 HUMAN_LONGEVITY ss2283631731 Dec 20, 2016 (150)
17 GNOMAD ss2735810610 Nov 08, 2017 (151)
18 GNOMAD ss2747630510 Nov 08, 2017 (151)
19 GNOMAD ss2838383193 Nov 08, 2017 (151)
20 ILLUMINA ss3022617474 Nov 08, 2017 (151)
21 ILLUMINA ss3629537209 Oct 12, 2018 (152)
22 ILLUMINA ss3629537210 Oct 12, 2018 (152)
23 ILLUMINA ss3635065948 Oct 12, 2018 (152)
24 ILLUMINA ss3638627953 Oct 12, 2018 (152)
25 ILLUMINA ss3640773247 Oct 12, 2018 (152)
26 ILLUMINA ss3643569224 Oct 12, 2018 (152)
27 ILLUMINA ss3644911645 Oct 12, 2018 (152)
28 ILLUMINA ss3653134128 Oct 12, 2018 (152)
29 ILLUMINA ss3726343778 Jul 13, 2019 (153)
30 ILLUMINA ss3744554561 Jul 13, 2019 (153)
31 ILLUMINA ss3745365887 Jul 13, 2019 (153)
32 PAGE_CC ss3771291177 Jul 13, 2019 (153)
33 ILLUMINA ss3772859451 Jul 13, 2019 (153)
34 EVA ss3824191604 Apr 26, 2020 (154)
35 EVA ss3984568569 Apr 26, 2021 (155)
36 EVA ss4017273051 Apr 26, 2021 (155)
37 TOPMED ss4701099539 Apr 26, 2021 (155)
38 EVA ss5315153409 Oct 13, 2022 (156)
39 EVA ss5365275357 Oct 13, 2022 (156)
40 HUGCELL_USP ss5465946522 Oct 13, 2022 (156)
41 EVA ss5848096443 Oct 13, 2022 (156)
42 EVA ss5968788351 Oct 13, 2022 (156)
43 ExAC NC_000006.11 - 43501664 Oct 12, 2018 (152)
44 gnomAD - Genomes NC_000006.12 - 43533927 Apr 26, 2021 (155)
45 gnomAD - Exomes NC_000006.11 - 43501664 Jul 13, 2019 (153)
46 GO Exome Sequencing Project NC_000006.11 - 43501664 Oct 12, 2018 (152)
47 The PAGE Study NC_000006.12 - 43533927 Jul 13, 2019 (153)
48 CNV burdens in cranial meningiomas NC_000006.11 - 43501664 Apr 26, 2021 (155)
49 Qatari NC_000006.11 - 43501664 Apr 26, 2020 (154)
50 TopMed NC_000006.12 - 43533927 Apr 26, 2021 (155)
51 ALFA NC_000006.12 - 43533927 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
ss3643569224 NC_000006.10:43609641:G:A NC_000006.12:43533926:G:A (self)
8368582, 4954536, 649621, 117977, 8172565, ss491386391, ss537181077, ss712712187, ss780849732, ss783533545, ss1688335311, ss1752638031, ss1917805935, ss1926130635, ss1946178590, ss1958906122, ss2735810610, ss2747630510, ss2838383193, ss3022617474, ss3629537209, ss3629537210, ss3635065948, ss3638627953, ss3640773247, ss3644911645, ss3653134128, ss3744554561, ss3745365887, ss3772859451, ss3824191604, ss3984568569, ss4017273051, ss5315153409, ss5365275357, ss5848096443, ss5968788351 NC_000006.11:43501663:G:A NC_000006.12:43533926:G:A (self)
223616980, 512646, 538477097, 4045660770, ss2283631731, ss3726343778, ss3771291177, ss4701099539, ss5465946522 NC_000006.12:43533926:G:A NC_000006.12:43533926:G:A (self)
ss48417284, ss74998094, ss119918859, ss173605095 NT_007592.15:43441663:G:A NC_000006.12:43533926:G:A (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs35794454
PMID Title Author Year Journal
21552306 Genetic and epigenetic association studies suggest a role of microRNA biogenesis gene exportin-5 (XPO5) in breast tumorigenesis. Leaderer D et al. 2011 International journal of molecular epidemiology and genetics
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