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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.

rs34796184

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:1103994-1104003 (GRCh38.p13) 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
delT / dupT / dupTT
Variation Type
Indel Insertion and Deletion
Frequency
dupT=0.04416 (518/11730, ALFA)
dupT=0.2825 (1415/5008, 1000G)
dupT=0.1251 (482/3854, ALSPAC) (+ 4 more)
dupT=0.1389 (515/3708, TWINSUK)
dupT=0.2320 (425/1832, Korea1K)
dupT=0.113 (68/600, NorthernSweden)
dupT=0.15 (6/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
C1orf159 : Intron Variant
Publications
0 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.p13 chr 1 NC_000001.11:g.1104003del
GRCh38.p13 chr 1 NC_000001.11:g.1104003dup
GRCh38.p13 chr 1 NC_000001.11:g.1104002_1104003dup
GRCh37.p13 chr 1 NC_000001.10:g.1039383del
GRCh37.p13 chr 1 NC_000001.10:g.1039383dup
GRCh37.p13 chr 1 NC_000001.10:g.1039382_1039383dup
Gene: C1orf159, chromosome 1 open reading frame 159 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
C1orf159 transcript variant 1 NM_001330306.2:c.-136+110…

NM_001330306.2:c.-136+11028del

N/A Intron Variant
C1orf159 transcript variant 3 NM_001363525.2:c.-136+110…

NM_001363525.2:c.-136+11028del

N/A Intron Variant
C1orf159 transcript variant 2 NM_017891.5:c.-135-11891d…

NM_017891.5:c.-135-11891del

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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 11730 TTTTTTTTTT=0.95575 TTTTTTTTT=0.00009, TTTTTTTTTTT=0.04416, TTTTTTTTTTTT=0.00000
European Sub 10030 TTTTTTTTTT=0.94826 TTTTTTTTT=0.00010, TTTTTTTTTTT=0.05165, TTTTTTTTTTTT=0.00000
African Sub 820 TTTTTTTTTT=1.000 TTTTTTTTT=0.000, TTTTTTTTTTT=0.000, TTTTTTTTTTTT=0.000
African Others Sub 22 TTTTTTTTTT=1.00 TTTTTTTTT=0.00, TTTTTTTTTTT=0.00, TTTTTTTTTTTT=0.00
African American Sub 798 TTTTTTTTTT=1.000 TTTTTTTTT=0.000, TTTTTTTTTTT=0.000, TTTTTTTTTTTT=0.000
Asian Sub 72 TTTTTTTTTT=1.00 TTTTTTTTT=0.00, TTTTTTTTTTT=0.00, TTTTTTTTTTTT=0.00
East Asian Sub 62 TTTTTTTTTT=1.00 TTTTTTTTT=0.00, TTTTTTTTTTT=0.00, TTTTTTTTTTTT=0.00
Other Asian Sub 10 TTTTTTTTTT=1.0 TTTTTTTTT=0.0, TTTTTTTTTTT=0.0, TTTTTTTTTTTT=0.0
Latin American 1 Sub 74 TTTTTTTTTT=1.00 TTTTTTTTT=0.00, TTTTTTTTTTT=0.00, TTTTTTTTTTTT=0.00
Latin American 2 Sub 410 TTTTTTTTTT=1.000 TTTTTTTTT=0.000, TTTTTTTTTTT=0.000, TTTTTTTTTTTT=0.000
South Asian Sub 66 TTTTTTTTTT=1.00 TTTTTTTTT=0.00, TTTTTTTTTTT=0.00, TTTTTTTTTTTT=0.00
Other Sub 258 TTTTTTTTTT=1.000 TTTTTTTTT=0.000, TTTTTTTTTTT=0.000, TTTTTTTTTTTT=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
1000Genomes Global Study-wide 5008 -

No frequency provided

dupT=0.2825
1000Genomes African Sub 1322 -

No frequency provided

dupT=0.5303
1000Genomes East Asian Sub 1008 -

No frequency provided

dupT=0.2232
1000Genomes Europe Sub 1006 -

No frequency provided

dupT=0.1352
1000Genomes South Asian Sub 978 -

No frequency provided

dupT=0.238
1000Genomes American Sub 694 -

No frequency provided

dupT=0.173
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 -

No frequency provided

dupT=0.1251
UK 10K study - Twins TWIN COHORT Study-wide 3708 -

No frequency provided

dupT=0.1389
Korean Genome Project KOREAN Study-wide 1832 -

No frequency provided

dupT=0.2320
Northern Sweden ACPOP Study-wide 600 -

No frequency provided

dupT=0.113
The Danish reference pan genome Danish Study-wide 40 -

No frequency provided

dupT=0.15
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)10= delT dupT dupTT
GRCh38.p13 chr 1 NC_000001.11:g.1103994_1104003= NC_000001.11:g.1104003del NC_000001.11:g.1104003dup NC_000001.11:g.1104002_1104003dup
GRCh37.p13 chr 1 NC_000001.10:g.1039374_1039383= NC_000001.10:g.1039383del NC_000001.10:g.1039383dup NC_000001.10:g.1039382_1039383dup
C1orf159 transcript variant 1 NM_001330306.2:c.-136+11028= NM_001330306.2:c.-136+11028del NM_001330306.2:c.-136+11019dup NM_001330306.2:c.-136+11019_-136+11020dup
C1orf159 transcript variant 3 NM_001363525.2:c.-136+11028= NM_001363525.2:c.-136+11028del NM_001363525.2:c.-136+11019dup NM_001363525.2:c.-136+11019_-136+11020dup
C1orf159 transcript variant 2 NM_017891.4:c.-135-11891= NM_017891.4:c.-135-11891del NM_017891.4:c.-135-11900dup NM_017891.4:c.-135-11900_-135-11899dup
C1orf159 transcript variant 2 NM_017891.5:c.-135-11891= NM_017891.5:c.-135-11891del NM_017891.5:c.-135-11900dup NM_017891.5:c.-135-11900_-135-11899dup
C1orf159 transcript variant X1 XM_005244764.1:c.-136+11028= XM_005244764.1:c.-136+11028del XM_005244764.1:c.-136+11019dup XM_005244764.1:c.-136+11019_-136+11020dup
C1orf159 transcript variant X16 XM_005244765.1:c.-135-11891= XM_005244765.1:c.-135-11891del XM_005244765.1:c.-135-11900dup XM_005244765.1:c.-135-11900_-135-11899dup
C1orf159 transcript variant X3 XM_005244766.1:c.-135-11891= XM_005244766.1:c.-135-11891del XM_005244766.1:c.-135-11900dup XM_005244766.1:c.-135-11900_-135-11899dup
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#.

38 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 ABI ss41099067 Oct 11, 2018 (152)
2 HUMANGENOME_JCVI ss95218989 Feb 06, 2009 (130)
3 HUMANGENOME_JCVI ss98565697 Feb 13, 2009 (138)
4 BUSHMAN ss193082085 Jul 04, 2010 (138)
5 GMI ss287939666 May 04, 2012 (137)
6 PJP ss294562412 May 09, 2011 (137)
7 PJP ss294562413 May 09, 2011 (137)
8 1000GENOMES ss325997324 May 09, 2011 (138)
9 1000GENOMES ss325997762 May 09, 2011 (138)
10 1000GENOMES ss498763989 May 04, 2012 (138)
11 LUNTER ss550899277 Apr 25, 2013 (138)
12 LUNTER ss552739241 Apr 25, 2013 (138)
13 SSMP ss663105531 Apr 01, 2015 (144)
14 1000GENOMES ss1367645826 Aug 21, 2014 (142)
15 EVA_GENOME_DK ss1573868718 Apr 01, 2015 (144)
16 EVA_UK10K_ALSPAC ss1700146177 Apr 01, 2015 (144)
17 EVA_UK10K_TWINSUK ss1700154942 Apr 01, 2015 (144)
18 JJLAB ss2030297882 Sep 14, 2016 (149)
19 SYSTEMSBIOZJU ss2624265492 Nov 08, 2017 (151)
20 SWEGEN ss2986154167 Nov 08, 2017 (151)
21 MCHAISSO ss3064386205 Nov 08, 2017 (151)
22 MCHAISSO ss3065282682 Nov 08, 2017 (151)
23 TOPMED ss3066468849 Nov 08, 2017 (151)
24 TOPMED ss3066468850 Nov 08, 2017 (151)
25 TOPMED ss3066468851 Nov 08, 2017 (151)
26 BIOINF_KMB_FNS_UNIBA ss3645022510 Oct 11, 2018 (152)
27 URBANLAB ss3646581885 Oct 11, 2018 (152)
28 EVA_DECODE ss3685997715 Jul 12, 2019 (153)
29 EVA_DECODE ss3685997716 Jul 12, 2019 (153)
30 ACPOP ss3726718586 Jul 12, 2019 (153)
31 KHV_HUMAN_GENOMES ss3798746748 Jul 12, 2019 (153)
32 EVA ss3825982549 Apr 25, 2020 (154)
33 KOGIC ss3943635966 Apr 25, 2020 (154)
34 GNOMAD ss3986967816 Apr 25, 2021 (155)
35 GNOMAD ss3986967817 Apr 25, 2021 (155)
36 GNOMAD ss3986967818 Apr 25, 2021 (155)
37 TOMMO_GENOMICS ss5142066247 Apr 25, 2021 (155)
38 TOMMO_GENOMICS ss5142066248 Apr 25, 2021 (155)
39 1000Genomes NC_000001.10 - 1039374 Oct 11, 2018 (152)
40 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 1039374 Oct 11, 2018 (152)
41 The Danish reference pan genome NC_000001.10 - 1039374 Apr 25, 2020 (154)
42 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 138210 (NC_000001.11:1103993::T 33418/137462)
Row 138211 (NC_000001.11:1103993::TT 104/137566)
Row 138212 (NC_000001.11:1103993:T: 8/137568)

- Apr 25, 2021 (155)
43 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 138210 (NC_000001.11:1103993::T 33418/137462)
Row 138211 (NC_000001.11:1103993::TT 104/137566)
Row 138212 (NC_000001.11:1103993:T: 8/137568)

- Apr 25, 2021 (155)
44 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 138210 (NC_000001.11:1103993::T 33418/137462)
Row 138211 (NC_000001.11:1103993::TT 104/137566)
Row 138212 (NC_000001.11:1103993:T: 8/137568)

- Apr 25, 2021 (155)
45 Korean Genome Project NC_000001.11 - 1103994 Apr 25, 2020 (154)
46 Northern Sweden NC_000001.10 - 1039374 Jul 12, 2019 (153)
47 8.3KJPN

Submission ignored due to conflicting rows:
Row 35554 (NC_000001.10:1039373::T 3444/16760)
Row 35555 (NC_000001.10:1039373::TT 5/16760)

- Apr 25, 2021 (155)
48 8.3KJPN

Submission ignored due to conflicting rows:
Row 35554 (NC_000001.10:1039373::T 3444/16760)
Row 35555 (NC_000001.10:1039373::TT 5/16760)

- Apr 25, 2021 (155)
49 UK 10K study - Twins NC_000001.10 - 1039374 Oct 11, 2018 (152)
50 ALFA NC_000001.11 - 1103994 Apr 25, 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)
rs71576599 May 15, 2013 (138)
rs140542667 May 11, 2012 (137)
rs150123792 Sep 17, 2011 (135)
rs151293107 May 11, 2012 (137)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3066468851, ss3685997715, ss3986967818 NC_000001.11:1103993:T: NC_000001.11:1103993:TTTTTTTTTT:TT…

NC_000001.11:1103993:TTTTTTTTTT:TTTTTTTTT

(self)
13775374401 NC_000001.11:1103993:TTTTTTTTTT:TT…

NC_000001.11:1103993:TTTTTTTTTT:TTTTTTTTT

NC_000001.11:1103993:TTTTTTTTTT:TT…

NC_000001.11:1103993:TTTTTTTTTT:TTTTTTTTT

ss325997324, ss325997762, ss550899277, ss552739241 NC_000001.9:1029236::T NC_000001.11:1103993:TTTTTTTTTT:TT…

NC_000001.11:1103993:TTTTTTTTTT:TTTTTTTTTTT

(self)
ss294562412 NC_000001.9:1029240::T NC_000001.11:1103993:TTTTTTTTTT:TT…

NC_000001.11:1103993:TTTTTTTTTT:TTTTTTTTTTT

(self)
ss294562413 NC_000001.9:1029243::T NC_000001.11:1103993:TTTTTTTTTT:TT…

NC_000001.11:1103993:TTTTTTTTTT:TTTTTTTTTTT

(self)
ss287939666 NC_000001.9:1029246::T NC_000001.11:1103993:TTTTTTTTTT:TT…

NC_000001.11:1103993:TTTTTTTTTT:TTTTTTTTTTT

(self)
14891, 4703, 120349, 3451, 4703, ss498763989, ss663105531, ss1367645826, ss1573868718, ss1700146177, ss1700154942, ss2030297882, ss2624265492, ss2986154167, ss3726718586, ss3825982549, ss5142066247 NC_000001.10:1039373::T NC_000001.11:1103993:TTTTTTTTTT:TT…

NC_000001.11:1103993:TTTTTTTTTT:TTTTTTTTTTT

(self)
13967, ss3064386205, ss3065282682, ss3066468849, ss3645022510, ss3646581885, ss3798746748, ss3943635966, ss3986967816 NC_000001.11:1103993::T NC_000001.11:1103993:TTTTTTTTTT:TT…

NC_000001.11:1103993:TTTTTTTTTT:TTTTTTTTTTT

(self)
13775374401 NC_000001.11:1103993:TTTTTTTTTT:TT…

NC_000001.11:1103993:TTTTTTTTTT:TTTTTTTTTTT

NC_000001.11:1103993:TTTTTTTTTT:TT…

NC_000001.11:1103993:TTTTTTTTTT:TTTTTTTTTTT

ss3685997716 NC_000001.11:1103994::T NC_000001.11:1103993:TTTTTTTTTT:TT…

NC_000001.11:1103993:TTTTTTTTTT:TTTTTTTTTTT

(self)
ss98565697 NT_004350.19:518005::T NC_000001.11:1103993:TTTTTTTTTT:TT…

NC_000001.11:1103993:TTTTTTTTTT:TTTTTTTTTTT

(self)
ss41099067, ss95218989 NT_004350.19:518015::T NC_000001.11:1103993:TTTTTTTTTT:TT…

NC_000001.11:1103993:TTTTTTTTTT:TTTTTTTTTTT

(self)
ss193082085 NT_032977.10:518005::T NC_000001.11:1103993:TTTTTTTTTT:TT…

NC_000001.11:1103993:TTTTTTTTTT:TTTTTTTTTTT

(self)
ss5142066248 NC_000001.10:1039373::TT NC_000001.11:1103993:TTTTTTTTTT:TT…

NC_000001.11:1103993:TTTTTTTTTT:TTTTTTTTTTTT

(self)
ss3066468850, ss3986967817 NC_000001.11:1103993::TT NC_000001.11:1103993:TTTTTTTTTT:TT…

NC_000001.11:1103993:TTTTTTTTTT:TTTTTTTTTTTT

(self)
13775374401 NC_000001.11:1103993:TTTTTTTTTT:TT…

NC_000001.11:1103993:TTTTTTTTTT:TTTTTTTTTTTT

NC_000001.11:1103993:TTTTTTTTTT:TT…

NC_000001.11:1103993:TTTTTTTTTT:TTTTTTTTTTTT

Removed from this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Destination RSIDs
NC_000001.10:1039373:T: NC_000001.11:1103993:TTTTTTTTTT:TT…

NC_000001.11:1103993:TTTTTTTTTT:TTTTTTTTT

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 rs34796184

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.post596+ae089ad