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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.

rs5805782

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr13:93058226-93058234 (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
delAA / delA / dupA / dupAA
Variation Type
Indel Insertion and Deletion
Frequency
(A)9=0.370244 (98000/264690, TOPMED)
delA=0.48598 (8145/16760, 8.3KJPN)
(A)9=0.4390 (3585/8166, ALFA) (+ 9 more)
(A)9=0.4129 (2068/5008, 1000G)
(A)9=0.3089 (1384/4480, Estonian)
(A)9=0.3179 (1225/3854, ALSPAC)
(A)9=0.3282 (1217/3708, TWINSUK)
(A)9=0.4558 (835/1832, Korea1K)
(A)9=0.277 (276/998, GoNL)
(A)9=0.287 (172/600, NorthernSweden)
(A)9=0.462 (97/210, Vietnamese)
(A)9=0.17 (7/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC00363 : 500B Downstream 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 8166 AAAAAAAAA=0.4390 AAAAAAA=0.0000, AAAAAAAA=0.5610, AAAAAAAAAA=0.0000, AAAAAAAAAAA=0.0000 0.265981 0.38795 0.346069 32
European Sub 7310 AAAAAAAAA=0.3841 AAAAAAA=0.0000, AAAAAAAA=0.6159, AAAAAAAAAA=0.0000, AAAAAAAAAAA=0.0000 0.194254 0.425992 0.379754 32
African Sub 586 AAAAAAAAA=0.913 AAAAAAA=0.000, AAAAAAAA=0.087, AAAAAAAAAA=0.000, AAAAAAAAAAA=0.000 0.887372 0.061433 0.051195 32
African Others Sub 38 AAAAAAAAA=0.89 AAAAAAA=0.00, AAAAAAAA=0.11, AAAAAAAAAA=0.00, AAAAAAAAAAA=0.00 0.842105 0.052632 0.105263 2
African American Sub 548 AAAAAAAAA=0.914 AAAAAAA=0.000, AAAAAAAA=0.086, AAAAAAAAAA=0.000, AAAAAAAAAAA=0.000 0.890511 0.062044 0.047445 32
Asian Sub 24 AAAAAAAAA=0.92 AAAAAAA=0.00, AAAAAAAA=0.08, AAAAAAAAAA=0.00, AAAAAAAAAAA=0.00 0.833333 0.0 0.166667 0
East Asian Sub 20 AAAAAAAAA=0.95 AAAAAAA=0.00, AAAAAAAA=0.05, AAAAAAAAAA=0.00, AAAAAAAAAAA=0.00 0.9 0.0 0.1 0
Other Asian Sub 4 AAAAAAAAA=0.8 AAAAAAA=0.0, AAAAAAAA=0.2, AAAAAAAAAA=0.0, AAAAAAAAAAA=0.0 0.5 0.0 0.5 0
Latin American 1 Sub 32 AAAAAAAAA=1.00 AAAAAAA=0.00, AAAAAAAA=0.00, AAAAAAAAAA=0.00, AAAAAAAAAAA=0.00 1.0 0.0 0.0 N/A
Latin American 2 Sub 76 AAAAAAAAA=1.00 AAAAAAA=0.00, AAAAAAAA=0.00, AAAAAAAAAA=0.00, AAAAAAAAAAA=0.00 1.0 0.0 0.0 N/A
South Asian Sub 30 AAAAAAAAA=0.93 AAAAAAA=0.00, AAAAAAAA=0.07, AAAAAAAAAA=0.00, AAAAAAAAAAA=0.00 0.866667 0.0 0.133333 0
Other Sub 108 AAAAAAAAA=0.778 AAAAAAA=0.000, AAAAAAAA=0.222, AAAAAAAAAA=0.000, AAAAAAAAAAA=0.000 0.722222 0.166667 0.111111 14


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)9=0.370244 delA=0.629756
8.3KJPN JAPANESE Study-wide 16760 (A)9=0.51402 delA=0.48598
Allele Frequency Aggregator Total Global 8166 (A)9=0.4390 delAA=0.0000, delA=0.5610, dupA=0.0000, dupAA=0.0000
Allele Frequency Aggregator European Sub 7310 (A)9=0.3841 delAA=0.0000, delA=0.6159, dupA=0.0000, dupAA=0.0000
Allele Frequency Aggregator African Sub 586 (A)9=0.913 delAA=0.000, delA=0.087, dupA=0.000, dupAA=0.000
Allele Frequency Aggregator Other Sub 108 (A)9=0.778 delAA=0.000, delA=0.222, dupA=0.000, dupAA=0.000
Allele Frequency Aggregator Latin American 2 Sub 76 (A)9=1.00 delAA=0.00, delA=0.00, dupA=0.00, dupAA=0.00
Allele Frequency Aggregator Latin American 1 Sub 32 (A)9=1.00 delAA=0.00, delA=0.00, dupA=0.00, dupAA=0.00
Allele Frequency Aggregator South Asian Sub 30 (A)9=0.93 delAA=0.00, delA=0.07, dupA=0.00, dupAA=0.00
Allele Frequency Aggregator Asian Sub 24 (A)9=0.92 delAA=0.00, delA=0.08, dupA=0.00, dupAA=0.00
1000Genomes Global Study-wide 5008 (A)9=0.4129 delA=0.5871
1000Genomes African Sub 1322 (A)9=0.4349 delA=0.5651
1000Genomes East Asian Sub 1008 (A)9=0.4325 delA=0.5675
1000Genomes Europe Sub 1006 (A)9=0.3340 delA=0.6660
1000Genomes South Asian Sub 978 (A)9=0.495 delA=0.505
1000Genomes American Sub 694 (A)9=0.341 delA=0.659
Genetic variation in the Estonian population Estonian Study-wide 4480 (A)9=0.3089 delA=0.6911
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 (A)9=0.3179 delA=0.6821
UK 10K study - Twins TWIN COHORT Study-wide 3708 (A)9=0.3282 delA=0.6718
Korean Genome Project KOREAN Study-wide 1832 (A)9=0.4558 delA=0.5442
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 (A)9=0.277 delA=0.723
Northern Sweden ACPOP Study-wide 600 (A)9=0.287 delA=0.713
A Vietnamese Genetic Variation Database Global Study-wide 210 (A)9=0.462 delA=0.538
The Danish reference pan genome Danish Study-wide 40 (A)9=0.17 delA=0.82
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.93058233_93058234del
GRCh38.p14 chr 13 NC_000013.11:g.93058234del
GRCh38.p14 chr 13 NC_000013.11:g.93058234dup
GRCh38.p14 chr 13 NC_000013.11:g.93058233_93058234dup
GRCh37.p13 chr 13 NC_000013.10:g.93710486_93710487del
GRCh37.p13 chr 13 NC_000013.10:g.93710487del
GRCh37.p13 chr 13 NC_000013.10:g.93710487dup
GRCh37.p13 chr 13 NC_000013.10:g.93710486_93710487dup
Gene: LINC00363, long intergenic non-protein coding RNA 363 (plus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
LINC00363 transcript NR_126360.1:n. N/A 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)9= delAA delA dupA dupAA
GRCh38.p14 chr 13 NC_000013.11:g.93058226_93058234= NC_000013.11:g.93058233_93058234del NC_000013.11:g.93058234del NC_000013.11:g.93058234dup NC_000013.11:g.93058233_93058234dup
GRCh37.p13 chr 13 NC_000013.10:g.93710479_93710487= NC_000013.10:g.93710486_93710487del NC_000013.10:g.93710487del NC_000013.10:g.93710487dup NC_000013.10:g.93710486_93710487dup
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#.

55 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 HUMANGENOME_JCVI ss95629424 Feb 04, 2009 (137)
2 HUMANGENOME_JCVI ss95768716 Feb 04, 2009 (137)
3 BUSHMAN ss193332618 Jul 04, 2010 (132)
4 GMI ss287910814 May 09, 2011 (134)
5 GMI ss289196493 May 04, 2012 (137)
6 PJP ss294813429 May 09, 2011 (134)
7 PJP ss294813430 May 09, 2011 (137)
8 1000GENOMES ss327559975 May 09, 2011 (137)
9 1000GENOMES ss327667614 May 09, 2011 (137)
10 1000GENOMES ss328107066 May 09, 2011 (137)
11 LUNTER ss552323926 Apr 25, 2013 (138)
12 LUNTER ss552637930 Apr 25, 2013 (138)
13 LUNTER ss553532450 Apr 25, 2013 (138)
14 SSMP ss664204799 Apr 01, 2015 (144)
15 BILGI_BIOE ss666611199 Apr 25, 2013 (138)
16 EVA-GONL ss990720622 Aug 21, 2014 (142)
17 1000GENOMES ss1373528705 Aug 21, 2014 (142)
18 EVA_GENOME_DK ss1574687687 Apr 01, 2015 (144)
19 EVA_UK10K_ALSPAC ss1707902969 Apr 01, 2015 (144)
20 EVA_UK10K_TWINSUK ss1707903082 Apr 01, 2015 (144)
21 HAMMER_LAB ss1807738801 Sep 08, 2015 (146)
22 JJLAB ss2031203906 Sep 14, 2016 (149)
23 SWEGEN ss3011514369 Nov 08, 2017 (151)
24 MCHAISSO ss3063777667 Nov 08, 2017 (151)
25 MCHAISSO ss3064610475 Nov 08, 2017 (151)
26 BEROUKHIMLAB ss3644365911 Oct 12, 2018 (152)
27 BIOINF_KMB_FNS_UNIBA ss3645322063 Oct 12, 2018 (152)
28 URBANLAB ss3650106521 Oct 12, 2018 (152)
29 EGCUT_WGS ss3678795963 Jul 13, 2019 (153)
30 EVA_DECODE ss3695887385 Jul 13, 2019 (153)
31 EVA_DECODE ss3695887386 Jul 13, 2019 (153)
32 ACPOP ss3740020541 Jul 13, 2019 (153)
33 PACBIO ss3787546731 Jul 13, 2019 (153)
34 PACBIO ss3792601008 Jul 13, 2019 (153)
35 PACBIO ss3797484770 Jul 13, 2019 (153)
36 KHV_HUMAN_GENOMES ss3817163547 Jul 13, 2019 (153)
37 EVA ss3833706789 Apr 27, 2020 (154)
38 EVA ss3840442461 Apr 27, 2020 (154)
39 EVA ss3845929797 Apr 27, 2020 (154)
40 KOGIC ss3974122758 Apr 27, 2020 (154)
41 GNOMAD ss4271199862 Apr 26, 2021 (155)
42 GNOMAD ss4271199863 Apr 26, 2021 (155)
43 GNOMAD ss4271199864 Apr 26, 2021 (155)
44 TOPMED ss4957122844 Apr 26, 2021 (155)
45 TOMMO_GENOMICS ss5211353607 Apr 26, 2021 (155)
46 1000G_HIGH_COVERAGE ss5294781430 Oct 16, 2022 (156)
47 HUGCELL_USP ss5489039397 Oct 16, 2022 (156)
48 SANFORD_IMAGENETICS ss5655384903 Oct 16, 2022 (156)
49 TOMMO_GENOMICS ss5763600143 Oct 16, 2022 (156)
50 TOMMO_GENOMICS ss5763600144 Oct 16, 2022 (156)
51 YY_MCH ss5814380588 Oct 16, 2022 (156)
52 EVA ss5839892443 Oct 16, 2022 (156)
53 EVA ss5850861080 Oct 16, 2022 (156)
54 EVA ss5926303543 Oct 16, 2022 (156)
55 EVA ss5946821719 Oct 16, 2022 (156)
56 1000Genomes NC_000013.10 - 93710479 Oct 12, 2018 (152)
57 The Avon Longitudinal Study of Parents and Children NC_000013.10 - 93710479 Oct 12, 2018 (152)
58 Genetic variation in the Estonian population NC_000013.10 - 93710479 Oct 12, 2018 (152)
59 The Danish reference pan genome NC_000013.10 - 93710479 Apr 27, 2020 (154)
60 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 439607273 (NC_000013.11:93058225::A 15/139676)
Row 439607274 (NC_000013.11:93058225::AA 3/139676)
Row 439607275 (NC_000013.11:93058225:A: 89407/139600)...

- Apr 26, 2021 (155)
61 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 439607273 (NC_000013.11:93058225::A 15/139676)
Row 439607274 (NC_000013.11:93058225::AA 3/139676)
Row 439607275 (NC_000013.11:93058225:A: 89407/139600)...

- Apr 26, 2021 (155)
62 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 439607273 (NC_000013.11:93058225::A 15/139676)
Row 439607274 (NC_000013.11:93058225::AA 3/139676)
Row 439607275 (NC_000013.11:93058225:A: 89407/139600)...

- Apr 26, 2021 (155)
63 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 439607273 (NC_000013.11:93058225::A 15/139676)
Row 439607274 (NC_000013.11:93058225::AA 3/139676)
Row 439607275 (NC_000013.11:93058225:A: 89407/139600)...

- Apr 26, 2021 (155)
64 Genome of the Netherlands Release 5 NC_000013.10 - 93710479 Apr 27, 2020 (154)
65 Korean Genome Project NC_000013.11 - 93058226 Apr 27, 2020 (154)
66 Northern Sweden NC_000013.10 - 93710479 Jul 13, 2019 (153)
67 8.3KJPN NC_000013.10 - 93710479 Apr 26, 2021 (155)
68 14KJPN

Submission ignored due to conflicting rows:
Row 97437247 (NC_000013.11:93058225:A: 13698/28256)
Row 97437248 (NC_000013.11:93058225::A 1/28256)

- Oct 16, 2022 (156)
69 14KJPN

Submission ignored due to conflicting rows:
Row 97437247 (NC_000013.11:93058225:A: 13698/28256)
Row 97437248 (NC_000013.11:93058225::A 1/28256)

- Oct 16, 2022 (156)
70 TopMed NC_000013.11 - 93058226 Apr 26, 2021 (155)
71 UK 10K study - Twins NC_000013.10 - 93710479 Oct 12, 2018 (152)
72 A Vietnamese Genetic Variation Database NC_000013.10 - 93710479 Jul 13, 2019 (153)
73 ALFA NC_000013.11 - 93058226 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)
rs66601122 May 11, 2012 (137)
rs66601123 Feb 26, 2009 (130)
rs66601124 Feb 26, 2009 (130)
rs66601125 Feb 26, 2009 (130)
rs138712318 May 04, 2012 (137)
rs374936618 May 13, 2013 (138)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss4271199864 NC_000013.11:93058225:AA: NC_000013.11:93058225:AAAAAAAAA:AA…

NC_000013.11:93058225:AAAAAAAAA:AAAAAAA

(self)
10394577449 NC_000013.11:93058225:AAAAAAAAA:AA…

NC_000013.11:93058225:AAAAAAAAA:AAAAAAA

NC_000013.11:93058225:AAAAAAAAA:AA…

NC_000013.11:93058225:AAAAAAAAA:AAAAAAA

(self)
ss289196493, ss294813429, ss327559975, ss327667614, ss328107066, ss552323926, ss552637930, ss553532450 NC_000013.9:92508479:A: NC_000013.11:93058225:AAAAAAAAA:AA…

NC_000013.11:93058225:AAAAAAAAA:AAAAAAAA

(self)
ss294813430 NC_000013.9:92508487:A: NC_000013.11:93058225:AAAAAAAAA:AA…

NC_000013.11:93058225:AAAAAAAAA:AAAAAAAA

(self)
62335581, 34632883, 24534211, 425312, 15465026, 13305406, 69322914, 34632883, 7698869, ss664204799, ss666611199, ss990720622, ss1373528705, ss1574687687, ss1707902969, ss1707903082, ss1807738801, ss2031203906, ss3011514369, ss3644365911, ss3678795963, ss3740020541, ss3787546731, ss3792601008, ss3797484770, ss3833706789, ss3840442461, ss5211353607, ss5655384903, ss5839892443, ss5946821719 NC_000013.10:93710478:A: NC_000013.11:93058225:AAAAAAAAA:AA…

NC_000013.11:93058225:AAAAAAAAA:AAAAAAAA

(self)
30500759, 172668502, ss3063777667, ss3064610475, ss3645322063, ss3650106521, ss3695887386, ss3817163547, ss3845929797, ss3974122758, ss4957122844, ss5294781430, ss5489039397, ss5763600143, ss5814380588, ss5850861080, ss5926303543 NC_000013.11:93058225:A: NC_000013.11:93058225:AAAAAAAAA:AA…

NC_000013.11:93058225:AAAAAAAAA:AAAAAAAA

(self)
10394577449 NC_000013.11:93058225:AAAAAAAAA:AA…

NC_000013.11:93058225:AAAAAAAAA:AAAAAAAA

NC_000013.11:93058225:AAAAAAAAA:AA…

NC_000013.11:93058225:AAAAAAAAA:AAAAAAAA

(self)
ss287910814 NT_009952.14:6800154:A: NC_000013.11:93058225:AAAAAAAAA:AA…

NC_000013.11:93058225:AAAAAAAAA:AAAAAAAA

(self)
ss95629424, ss95768716 NT_009952.14:6800162:A: NC_000013.11:93058225:AAAAAAAAA:AA…

NC_000013.11:93058225:AAAAAAAAA:AAAAAAAA

(self)
ss193332618 NT_009952.15:6805246:A: NC_000013.11:93058225:AAAAAAAAA:AA…

NC_000013.11:93058225:AAAAAAAAA:AAAAAAAA

(self)
ss4271199862, ss5763600144 NC_000013.11:93058225::A NC_000013.11:93058225:AAAAAAAAA:AA…

NC_000013.11:93058225:AAAAAAAAA:AAAAAAAAAA

(self)
10394577449 NC_000013.11:93058225:AAAAAAAAA:AA…

NC_000013.11:93058225:AAAAAAAAA:AAAAAAAAAA

NC_000013.11:93058225:AAAAAAAAA:AA…

NC_000013.11:93058225:AAAAAAAAA:AAAAAAAAAA

(self)
ss3695887385 NC_000013.11:93058226::A NC_000013.11:93058225:AAAAAAAAA:AA…

NC_000013.11:93058225:AAAAAAAAA:AAAAAAAAAA

(self)
ss4271199863 NC_000013.11:93058225::AA NC_000013.11:93058225:AAAAAAAAA:AA…

NC_000013.11:93058225:AAAAAAAAA:AAAAAAAAAAA

(self)
10394577449 NC_000013.11:93058225:AAAAAAAAA:AA…

NC_000013.11:93058225:AAAAAAAAA:AAAAAAAAAAA

NC_000013.11:93058225:AAAAAAAAA:AA…

NC_000013.11:93058225:AAAAAAAAA:AAAAAAAAAAA

(self)
Removed from this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Destination RSIDs
ss2363027034 NC_000013.10:93710478::AA NC_000013.11:93058225:AAAAAAAAA:AA…

NC_000013.11:93058225:AAAAAAAAA:AAAAAAAAAAA

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 rs5805782

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.post820+afb47a3d