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dbSNP Short Genetic Variations

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.

rs3797179

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr5:6666809 (GRCh38.p12) 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=0.11815 (14836/125568, TOPMED)
A=0.1276 (3947/30926, GnomAD)
A=0.118 (591/5008, 1000G) (+ 3 more)
A=0.159 (712/4480, Estonian)
A=0.131 (506/3854, ALSPAC)
A=0.132 (490/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SRD5A1 : Intron Variant
Publications
3 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.p12 chr 5 NC_000005.10:g.6666809G>A
GRCh37.p13 chr 5 NC_000005.9:g.6666922G>A
Gene: SRD5A1, steroid 5 alpha-reductase 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SRD5A1 transcript variant 1 NM_001047.3:c. N/A Intron Variant
SRD5A1 transcript variant 2 NM_001324322.1:c. N/A Intron Variant
SRD5A1 transcript variant 3 NM_001324323.1:c. N/A Intron Variant
SRD5A1 transcript variant 4 NR_136739.1:n. 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
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").

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Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 G=0.88185 A=0.11815
gnomAD - Genomes Global Study-wide 30926 G=0.8724 A=0.1276
gnomAD - Genomes European Sub 18484 G=0.8532 A=0.1468
gnomAD - Genomes African Sub 8714 G=0.926 A=0.074
gnomAD - Genomes East Asian Sub 1610 G=0.781 A=0.219
gnomAD - Genomes Other Sub 980 G=0.88 A=0.12
gnomAD - Genomes American Sub 838 G=0.91 A=0.09
gnomAD - Genomes Ashkenazi Jewish Sub 300 G=0.86 A=0.14
1000Genomes Global Study-wide 5008 G=0.882 A=0.118
1000Genomes African Sub 1322 G=0.938 A=0.062
1000Genomes East Asian Sub 1008 G=0.792 A=0.208
1000Genomes Europe Sub 1006 G=0.853 A=0.147
1000Genomes South Asian Sub 978 G=0.92 A=0.08
1000Genomes American Sub 694 G=0.90 A=0.10
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.841 A=0.159
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.869 A=0.131
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.868 A=0.132
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 Note
GRCh38.p12 chr 5 NC_000005.10:g.6666809G= NC_000005.10:g.6666809G>A
GRCh37.p13 chr 5 NC_000005.9:g.6666922G= NC_000005.9:g.6666922G>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#.

81 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss4983557 Aug 28, 2002 (107)
2 WI_SSAHASNP ss11718269 Jul 11, 2003 (116)
3 EGP_SNPS ss12586388 Aug 26, 2003 (117)
4 ILLUMINA ss66649248 Nov 30, 2006 (127)
5 ILLUMINA ss67304165 Nov 30, 2006 (127)
6 ILLUMINA ss67709196 Nov 30, 2006 (127)
7 ILLUMINA ss70782817 May 25, 2008 (130)
8 ILLUMINA ss71359385 May 17, 2007 (127)
9 ILLUMINA ss75517321 Dec 06, 2007 (129)
10 ILLUMINA ss79168060 Dec 15, 2007 (130)
11 KRIBB_YJKIM ss84188383 Dec 15, 2007 (130)
12 BGI ss104164729 Dec 01, 2009 (131)
13 1000GENOMES ss108777649 Jan 23, 2009 (130)
14 ILLUMINA ss122227719 Dec 01, 2009 (131)
15 ILLUMINA ss154270389 Dec 01, 2009 (131)
16 ILLUMINA ss159447145 Dec 01, 2009 (131)
17 ILLUMINA ss160643411 Dec 01, 2009 (131)
18 ILLUMINA ss171663987 Jul 04, 2010 (132)
19 ILLUMINA ss173643342 Jul 04, 2010 (132)
20 BUSHMAN ss199837524 Jul 04, 2010 (132)
21 1000GENOMES ss232814141 Jul 14, 2010 (132)
22 1000GENOMES ss240014751 Jul 15, 2010 (132)
23 BL ss253196496 May 09, 2011 (134)
24 GMI ss278153750 May 04, 2012 (137)
25 GMI ss285112269 Apr 25, 2013 (138)
26 ILLUMINA ss480838745 May 04, 2012 (137)
27 ILLUMINA ss480855377 May 04, 2012 (137)
28 ILLUMINA ss481788333 Sep 08, 2015 (146)
29 ILLUMINA ss485214210 May 04, 2012 (137)
30 ILLUMINA ss537195962 Sep 08, 2015 (146)
31 TISHKOFF ss558181356 Apr 25, 2013 (138)
32 SSMP ss652025884 Apr 25, 2013 (138)
33 ILLUMINA ss779041762 Sep 08, 2015 (146)
34 ILLUMINA ss783053068 Sep 08, 2015 (146)
35 ILLUMINA ss784011519 Sep 08, 2015 (146)
36 ILLUMINA ss825498578 Apr 01, 2015 (144)
37 ILLUMINA ss832310946 Sep 08, 2015 (146)
38 ILLUMINA ss834504614 Sep 08, 2015 (146)
39 EVA-GONL ss981214579 Aug 21, 2014 (142)
40 JMKIDD_LAB ss1072364240 Aug 21, 2014 (142)
41 1000GENOMES ss1313782119 Aug 21, 2014 (142)
42 DDI ss1430234433 Apr 01, 2015 (144)
43 EVA_GENOME_DK ss1580997027 Apr 01, 2015 (144)
44 EVA_DECODE ss1590730292 Apr 01, 2015 (144)
45 EVA_UK10K_ALSPAC ss1612208794 Apr 01, 2015 (144)
46 EVA_UK10K_TWINSUK ss1655202827 Apr 01, 2015 (144)
47 EVA_SVP ss1712741231 Apr 01, 2015 (144)
48 ILLUMINA ss1752581973 Sep 08, 2015 (146)
49 WEILL_CORNELL_DGM ss1924473328 Feb 12, 2016 (147)
50 ILLUMINA ss1958764211 Feb 12, 2016 (147)
51 JJLAB ss2022832010 Sep 14, 2016 (149)
52 USC_VALOUEV ss2150982619 Dec 20, 2016 (150)
53 HUMAN_LONGEVITY ss2271124283 Dec 20, 2016 (150)
54 TOPMED ss2439109995 Dec 20, 2016 (150)
55 SYSTEMSBIOZJU ss2625915448 Nov 08, 2017 (151)
56 ILLUMINA ss2634241531 Nov 08, 2017 (151)
57 GRF ss2706506350 Nov 08, 2017 (151)
58 ILLUMINA ss2711029596 Nov 08, 2017 (151)
59 GNOMAD ss2820808120 Nov 08, 2017 (151)
60 AFFY ss2985943262 Nov 08, 2017 (151)
61 SWEGEN ss2996387937 Nov 08, 2017 (151)
62 BIOINF_KMB_FNS_UNIBA ss3025200358 Nov 08, 2017 (151)
63 CSHL ss3346226167 Nov 08, 2017 (151)
64 TOPMED ss3455436487 Nov 08, 2017 (151)
65 ILLUMINA ss3625865433 Oct 12, 2018 (152)
66 ILLUMINA ss3629170731 Oct 12, 2018 (152)
67 ILLUMINA ss3632170527 Oct 12, 2018 (152)
68 ILLUMINA ss3633364318 Oct 12, 2018 (152)
69 ILLUMINA ss3634084510 Oct 12, 2018 (152)
70 ILLUMINA ss3634989763 Oct 12, 2018 (152)
71 ILLUMINA ss3635766766 Oct 12, 2018 (152)
72 ILLUMINA ss3636698916 Oct 12, 2018 (152)
73 ILLUMINA ss3637519370 Oct 12, 2018 (152)
74 ILLUMINA ss3638536606 Oct 12, 2018 (152)
75 ILLUMINA ss3639270894 Oct 12, 2018 (152)
76 ILLUMINA ss3639658230 Oct 12, 2018 (152)
77 ILLUMINA ss3640697056 Oct 12, 2018 (152)
78 ILLUMINA ss3641173360 Oct 12, 2018 (152)
79 ILLUMINA ss3641470355 Oct 12, 2018 (152)
80 ILLUMINA ss3643483868 Oct 12, 2018 (152)
81 ILLUMINA ss3644870567 Oct 12, 2018 (152)
82 1000Genomes NC_000005.9 - 6666922 Oct 12, 2018 (152)
83 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 6666922 Oct 12, 2018 (152)
84 Genetic variation in the Estonian population NC_000005.9 - 6666922 Oct 12, 2018 (152)
85 gnomAD - Genomes NC_000005.9 - 6666922 Oct 12, 2018 (152)
86 TopMed NC_000005.10 - 6666809 Oct 12, 2018 (152)
87 UK 10K study - Twins NC_000005.9 - 6666922 Oct 12, 2018 (152)
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)
rs59887933 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss108777649, ss199837524, ss253196496, ss278153750, ss285112269, ss480838745, ss825498578, ss1590730292, ss1712741231, ss3639270894, ss3639658230, ss3643483868 NC_000005.8:6719921:G= NC_000005.10:6666808:G= (self)
25332419, 14093013, 10015884, 161435876, 14093013, ss232814141, ss240014751, ss480855377, ss481788333, ss485214210, ss537195962, ss558181356, ss652025884, ss779041762, ss783053068, ss784011519, ss832310946, ss834504614, ss981214579, ss1072364240, ss1313782119, ss1430234433, ss1580997027, ss1612208794, ss1655202827, ss1752581973, ss1924473328, ss1958764211, ss2022832010, ss2150982619, ss2439109995, ss2625915448, ss2634241531, ss2706506350, ss2711029596, ss2820808120, ss2985943262, ss2996387937, ss3346226167, ss3625865433, ss3629170731, ss3632170527, ss3633364318, ss3634084510, ss3634989763, ss3635766766, ss3636698916, ss3637519370, ss3638536606, ss3640697056, ss3641173360, ss3641470355, ss3644870567 NC_000005.9:6666921:G= NC_000005.10:6666808:G= (self)
303801989, ss2271124283, ss3025200358, ss3455436487 NC_000005.10:6666808:G= NC_000005.10:6666808:G= (self)
ss4983557, ss12586388, ss66649248, ss67304165, ss67709196, ss70782817, ss71359385, ss75517321, ss79168060, ss84188383, ss104164729, ss122227719, ss154270389, ss159447145, ss160643411, ss171663987, ss173643342 NT_006576.16:6656921:G= NC_000005.10:6666808:G= (self)
ss11718269 NT_023089.13:6649659:G= NC_000005.10:6666808:G= (self)
ss108777649, ss199837524, ss253196496, ss278153750, ss285112269, ss480838745, ss825498578, ss1590730292, ss1712741231, ss3639270894, ss3639658230, ss3643483868 NC_000005.8:6719921:G>A NC_000005.10:6666808:G>A (self)
25332419, 14093013, 10015884, 161435876, 14093013, ss232814141, ss240014751, ss480855377, ss481788333, ss485214210, ss537195962, ss558181356, ss652025884, ss779041762, ss783053068, ss784011519, ss832310946, ss834504614, ss981214579, ss1072364240, ss1313782119, ss1430234433, ss1580997027, ss1612208794, ss1655202827, ss1752581973, ss1924473328, ss1958764211, ss2022832010, ss2150982619, ss2439109995, ss2625915448, ss2634241531, ss2706506350, ss2711029596, ss2820808120, ss2985943262, ss2996387937, ss3346226167, ss3625865433, ss3629170731, ss3632170527, ss3633364318, ss3634084510, ss3634989763, ss3635766766, ss3636698916, ss3637519370, ss3638536606, ss3640697056, ss3641173360, ss3641470355, ss3644870567 NC_000005.9:6666921:G>A NC_000005.10:6666808:G>A (self)
303801989, ss2271124283, ss3025200358, ss3455436487 NC_000005.10:6666808:G>A NC_000005.10:6666808:G>A (self)
ss4983557, ss12586388, ss66649248, ss67304165, ss67709196, ss70782817, ss71359385, ss75517321, ss79168060, ss84188383, ss104164729, ss122227719, ss154270389, ss159447145, ss160643411, ss171663987, ss173643342 NT_006576.16:6656921:G>A NC_000005.10:6666808:G>A (self)
ss11718269 NT_023089.13:6649659:G>A NC_000005.10:6666808: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.

3 citations for rs3797179
PMID Title Author Year Journal
18603647 Functional genetic polymorphisms and female reproductive disorders: Part I: Polycystic ovary syndrome and ovarian response. Simoni M et al. 2008 Human reproduction update
20200332 Family-based analysis of candidate genes for polycystic ovary syndrome. Ewens KG et al. 2010 The Journal of clinical endocrinology and metabolism
21530059 Association of genetic variants in the two isoforms of 5α-reductase, SRD5A1 and SRD5A2, in lean patients with polycystic ovary syndrome. Graupp M et al. 2011 European journal of obstetrics, gynecology, and reproductive biology

Genomic regions, transcripts, and products
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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.post76+b4aec9c