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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.


Current Build 155

Released April 9, 2021

Homo sapiens
chr1:1115167-1115168 (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.

Variation Type
Indel Insertion and Deletion
dupT=0.144599 (38274/264690, TOPMED)
dupT=0.142606 (19958/139952, GnomAD)
dupT=0.09465 (1753/18520, ALFA) (+ 8 more)
dupT=0.00078 (13/16760, 8.3KJPN)
dupT=0.1444 (723/5008, 1000G)
dupT=0.0473 (212/4480, Estonian)
dupT=0.0244 (94/3854, ALSPAC)
dupT=0.0224 (83/3708, TWINSUK)
dupT=0.0011 (2/1832, Korea1K)
dupT=0.027 (16/600, NorthernSweden)
dupT=0.03 (1/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
C1orf159 : Intron Variant
0 citations
Genomic View
See rs on genome

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.1115168dup
GRCh37.p13 chr 1 NC_000001.10:g.1050548dup
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.-189-93d…


N/A Intron Variant
C1orf159 transcript variant 3 NM_001363525.2:c.-189-93d…


N/A Intron Variant
C1orf159 transcript variant 2 NM_017891.5:c.-136+892dup N/A Intron Variant

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 18520 TT=0.90535 TTT=0.09465
European Sub 14152 TT=0.96559 TTT=0.03441
African Sub 2898 TT=0.6032 TTT=0.3968
African Others Sub 114 TT=0.482 TTT=0.518
African American Sub 2784 TT=0.6081 TTT=0.3919
Asian Sub 112 TT=0.991 TTT=0.009
East Asian Sub 86 TT=1.00 TTT=0.00
Other Asian Sub 26 TT=0.96 TTT=0.04
Latin American 1 Sub 146 TT=0.829 TTT=0.171
Latin American 2 Sub 610 TT=0.967 TTT=0.033
South Asian Sub 98 TT=0.99 TTT=0.01
Other Sub 504 TT=0.863 TTT=0.137


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").

Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 -

No frequency provided

gnomAD - Genomes Global Study-wide 139952 -

No frequency provided

gnomAD - Genomes European Sub 75876 -

No frequency provided

gnomAD - Genomes African Sub 41812 -

No frequency provided

gnomAD - Genomes American Sub 13664 -

No frequency provided

gnomAD - Genomes Ashkenazi Jewish Sub 3324 -

No frequency provided

gnomAD - Genomes East Asian Sub 3132 -

No frequency provided

gnomAD - Genomes Other Sub 2144 -

No frequency provided

8.3KJPN JAPANESE Study-wide 16760 -

No frequency provided

1000Genomes Global Study-wide 5008 -

No frequency provided

1000Genomes African Sub 1322 -

No frequency provided

1000Genomes East Asian Sub 1008 -

No frequency provided

1000Genomes Europe Sub 1006 -

No frequency provided

1000Genomes South Asian Sub 978 -

No frequency provided

1000Genomes American Sub 694 -

No frequency provided

Genetic variation in the Estonian population Estonian Study-wide 4480 -

No frequency provided

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

No frequency provided

UK 10K study - Twins TWIN COHORT Study-wide 3708 -

No frequency provided

Korean Genome Project KOREAN Study-wide 1832 -

No frequency provided

Northern Sweden ACPOP Study-wide 600 -

No frequency provided

The Danish reference pan genome Danish Study-wide 40 -

No frequency provided


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 TT= dupT
GRCh38.p13 chr 1 NC_000001.11:g.1115167_1115168= NC_000001.11:g.1115168dup
GRCh37.p13 chr 1 NC_000001.10:g.1050547_1050548= NC_000001.10:g.1050548dup
C1orf159 transcript variant 1 NM_001330306.2:c.-189-92= NM_001330306.2:c.-189-93dup
C1orf159 transcript variant 3 NM_001363525.2:c.-189-92= NM_001363525.2:c.-189-93dup
C1orf159 transcript variant 2 NM_017891.4:c.-136+893= NM_017891.4:c.-136+892dup
C1orf159 transcript variant 2 NM_017891.5:c.-136+893= NM_017891.5:c.-136+892dup
C1orf159 transcript variant X1 XM_005244764.1:c.-189-92= XM_005244764.1:c.-189-93dup
C1orf159 transcript variant X16 XM_005244765.1:c.-136+893= XM_005244765.1:c.-136+892dup
C1orf159 transcript variant X3 XM_005244766.1:c.-136+893= XM_005244766.1:c.-136+892dup

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#.

27 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 BUSHMAN ss193082093 Jul 04, 2010 (132)
2 1000GENOMES ss325997334 May 09, 2011 (135)
3 LUNTER ss550899284 Apr 25, 2013 (138)
4 TISHKOFF ss553747629 Apr 25, 2013 (138)
5 SSMP ss663106167 Apr 01, 2015 (144)
6 EVA-GONL ss974771976 Aug 21, 2014 (142)
7 1000GENOMES ss1367645840 Aug 21, 2014 (142)
8 DDI ss1536213985 Apr 01, 2015 (144)
9 EVA_GENOME_DK ss1573868720 Apr 01, 2015 (144)
10 EVA_DECODE ss1584131905 Apr 01, 2015 (144)
11 EVA_UK10K_ALSPAC ss1700146417 Apr 01, 2015 (144)
12 EVA_UK10K_TWINSUK ss1700154977 Apr 01, 2015 (144)
13 HAMMER_LAB ss1793716947 Sep 08, 2015 (146)
14 JJLAB ss2030297885 Sep 14, 2016 (149)
15 TOPMED ss2321525284 Dec 20, 2016 (150)
16 GNOMAD ss2750671586 Nov 08, 2017 (151)
17 SWEGEN ss2986154348 Nov 08, 2017 (151)
18 MCHAISSO ss3065282691 Nov 08, 2017 (151)
19 TOPMED ss3066471447 Nov 08, 2017 (151)
20 BIOINF_KMB_FNS_UNIBA ss3645022511 Oct 11, 2018 (152)
21 EGCUT_WGS ss3654265420 Jul 12, 2019 (153)
22 EVA_DECODE ss3685997918 Jul 12, 2019 (153)
23 ACPOP ss3726718675 Jul 12, 2019 (153)
24 KHV_HUMAN_GENOMES ss3798746874 Jul 12, 2019 (153)
25 KOGIC ss3943636246 Apr 25, 2020 (154)
26 TOPMED ss4436519199 Apr 25, 2021 (155)
27 TOMMO_GENOMICS ss5142066831 Apr 25, 2021 (155)
28 1000Genomes NC_000001.10 - 1050547 Oct 11, 2018 (152)
29 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 1050547 Oct 11, 2018 (152)
30 Genetic variation in the Estonian population NC_000001.10 - 1050547 Oct 11, 2018 (152)
31 The Danish reference pan genome NC_000001.10 - 1050547 Apr 25, 2020 (154)
32 gnomAD - Genomes NC_000001.11 - 1115167 Apr 25, 2021 (155)
33 Korean Genome Project NC_000001.11 - 1115167 Apr 25, 2020 (154)
34 Northern Sweden NC_000001.10 - 1050547 Jul 12, 2019 (153)
35 8.3KJPN NC_000001.10 - 1050547 Apr 25, 2021 (155)
36 TopMed NC_000001.11 - 1115167 Apr 25, 2021 (155)
37 UK 10K study - Twins NC_000001.10 - 1050547 Oct 11, 2018 (152)
38 ALFA NC_000001.11 - 1115167 Apr 25, 2021 (155)

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)
rs139798503 Sep 17, 2011 (135)
rs372405445 May 15, 2013 (138)
rs372485818 May 15, 2013 (138)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss325997334, ss550899284, ss1584131905 NC_000001.9:1040409::T NC_000001.11:1115166:TT:TTT (self)
15342, 4919, 3668, 120350, 3540, 36138, 4919, ss663106167, ss974771976, ss1367645840, ss1536213985, ss1573868720, ss1700146417, ss1700154977, ss1793716947, ss2030297885, ss2321525284, ss2750671586, ss2986154348, ss3654265420, ss3726718675, ss5142066831 NC_000001.10:1050546::T NC_000001.11:1115166:TT:TTT (self)
ss553747629 NC_000001.10:1050548::T NC_000001.11:1115166:TT:TTT (self)
141059, 14247, 70908, 125534, ss3065282691, ss3066471447, ss3645022511, ss3685997918, ss3798746874, ss3943636246, ss4436519199 NC_000001.11:1115166::T NC_000001.11:1115166:TT:TTT (self)
14639149529 NC_000001.11:1115166:TT:TTT NC_000001.11:1115166:TT:TTT (self)
ss193082093 NT_032977.10:529178::T NC_000001.11:1115166:TT:TTT (self)

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

No publications for rs111382468


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