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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.

rs113385670

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:1081645-1081648 (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
delG / dupG / dupGG / dupGGG / dup…

delG / dupG / dupGG / dupGGG / dup(G)4

Variation Type
Indel Insertion and Deletion
Frequency
dupG=0.00441 (65/14733, ALFA)
dupG=0.0145 (65/4476, Estonian)
dupG=0.0503 (90/1788, Korea1K) (+ 1 more)
dupG=0.012 (7/600, NorthernSweden)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
C1orf159 : 500B Downstream 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.1081648del
GRCh38.p13 chr 1 NC_000001.11:g.1081648dup
GRCh38.p13 chr 1 NC_000001.11:g.1081647_1081648dup
GRCh38.p13 chr 1 NC_000001.11:g.1081646_1081648dup
GRCh38.p13 chr 1 NC_000001.11:g.1081645_1081648dup
GRCh37.p13 chr 1 NC_000001.10:g.1017028del
GRCh37.p13 chr 1 NC_000001.10:g.1017028dup
GRCh37.p13 chr 1 NC_000001.10:g.1017027_1017028dup
GRCh37.p13 chr 1 NC_000001.10:g.1017026_1017028dup
GRCh37.p13 chr 1 NC_000001.10:g.1017025_1017028dup
Gene: C1orf159, chromosome 1 open reading frame 159 (minus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
C1orf159 transcript variant 1 NM_001330306.2:c. N/A Downstream Transcript Variant
C1orf159 transcript variant 3 NM_001363525.2:c. N/A Downstream Transcript Variant
C1orf159 transcript variant 2 NM_017891.5:c. 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

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 14733 GGGG=0.99559 GGGGG=0.00441, GGGGGG=0.00000, GGGGGGG=0.00000, GGGGGGGG=0.00000
European Sub 11737 GGGG=0.99446 GGGGG=0.00554, GGGGGG=0.00000, GGGGGGG=0.00000, GGGGGGGG=0.00000
African Sub 1704 GGGG=1.0000 GGGGG=0.0000, GGGGGG=0.0000, GGGGGGG=0.0000, GGGGGGGG=0.0000
African Others Sub 56 GGGG=1.00 GGGGG=0.00, GGGGGG=0.00, GGGGGGG=0.00, GGGGGGGG=0.00
African American Sub 1648 GGGG=1.0000 GGGGG=0.0000, GGGGGG=0.0000, GGGGGGG=0.0000, GGGGGGGG=0.0000
Asian Sub 98 GGGG=1.00 GGGGG=0.00, GGGGGG=0.00, GGGGGGG=0.00, GGGGGGGG=0.00
East Asian Sub 80 GGGG=1.00 GGGGG=0.00, GGGGGG=0.00, GGGGGGG=0.00, GGGGGGGG=0.00
Other Asian Sub 18 GGGG=1.00 GGGGG=0.00, GGGGGG=0.00, GGGGGGG=0.00, GGGGGGGG=0.00
Latin American 1 Sub 130 GGGG=1.000 GGGGG=0.000, GGGGGG=0.000, GGGGGGG=0.000, GGGGGGGG=0.000
Latin American 2 Sub 572 GGGG=1.000 GGGGG=0.000, GGGGGG=0.000, GGGGGGG=0.000, GGGGGGGG=0.000
South Asian Sub 88 GGGG=1.00 GGGGG=0.00, GGGGGG=0.00, GGGGGGG=0.00, GGGGGGGG=0.00
Other Sub 404 GGGG=1.000 GGGGG=0.000, GGGGGG=0.000, GGGGGGG=0.000, GGGGGGGG=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
Genetic variation in the Estonian population Estonian Study-wide 4476 -

No frequency provided

dupG=0.0145
Korean Genome Project KOREAN Study-wide 1788 -

No frequency provided

dupG=0.0503
Northern Sweden ACPOP Study-wide 600 -

No frequency provided

dupG=0.012
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)4= delG dupG dupGG dupGGG dup(G)4
GRCh38.p13 chr 1 NC_000001.11:g.1081645_1081648= NC_000001.11:g.1081648del NC_000001.11:g.1081648dup NC_000001.11:g.1081647_1081648dup NC_000001.11:g.1081646_1081648dup NC_000001.11:g.1081645_1081648dup
GRCh37.p13 chr 1 NC_000001.10:g.1017025_1017028= NC_000001.10:g.1017028del NC_000001.10:g.1017028dup NC_000001.10:g.1017027_1017028dup NC_000001.10:g.1017026_1017028dup NC_000001.10:g.1017025_1017028dup
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#.

30 SubSNP, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 BUSHMAN ss193082067 Jul 04, 2010 (132)
2 1000GENOMES ss325997312 May 09, 2011 (135)
3 1000GENOMES ss498763980 May 04, 2012 (137)
4 LUNTER ss550899271 Apr 25, 2013 (138)
5 EVA_UK10K_ALSPAC ss1700145909 Apr 01, 2015 (144)
6 EVA_UK10K_TWINSUK ss1700154876 Apr 01, 2015 (144)
7 EVA_UK10K_TWINSUK ss1709905415 Apr 01, 2015 (144)
8 EVA_UK10K_ALSPAC ss1709907376 Apr 01, 2015 (144)
9 SWEGEN ss2986153778 Nov 08, 2017 (151)
10 TOPMED ss3066463475 Nov 08, 2017 (151)
11 TOPMED ss3066463476 Nov 08, 2017 (151)
12 TOPMED ss3066463477 Nov 08, 2017 (151)
13 EGCUT_WGS ss3654264878 Jul 12, 2019 (153)
14 EVA_DECODE ss3685997259 Jul 12, 2019 (153)
15 EVA_DECODE ss3685997260 Jul 12, 2019 (153)
16 EVA_DECODE ss3685997261 Jul 12, 2019 (153)
17 ACPOP ss3726718407 Jul 12, 2019 (153)
18 PACBIO ss3783302995 Jul 12, 2019 (153)
19 PACBIO ss3788980782 Jul 12, 2019 (153)
20 PACBIO ss3788980783 Jul 12, 2019 (153)
21 PACBIO ss3793853331 Jul 12, 2019 (153)
22 PACBIO ss3793853332 Jul 12, 2019 (153)
23 EVA ss3825982463 Apr 25, 2020 (154)
24 KOGIC ss3943635434 Apr 25, 2020 (154)
25 GNOMAD ss3986964738 Apr 25, 2021 (155)
26 GNOMAD ss3986964739 Apr 25, 2021 (155)
27 GNOMAD ss3986964740 Apr 25, 2021 (155)
28 GNOMAD ss3986964741 Apr 25, 2021 (155)
29 TOMMO_GENOMICS ss5142065215 Apr 25, 2021 (155)
30 TOMMO_GENOMICS ss5142065216 Apr 25, 2021 (155)
31 The Avon Longitudinal Study of Parents and Children

Submission ignored due to conflicting rows:
Row 4191 (NC_000001.10:1017024:G: 656/3854)
Row 4192 (NC_000001.10:1017024::G 117/3854)

- Oct 11, 2018 (152)
32 The Avon Longitudinal Study of Parents and Children

Submission ignored due to conflicting rows:
Row 4191 (NC_000001.10:1017024:G: 656/3854)
Row 4192 (NC_000001.10:1017024::G 117/3854)

- Oct 11, 2018 (152)
33 Genetic variation in the Estonian population NC_000001.10 - 1017025 Oct 11, 2018 (152)
34 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 132379 (NC_000001.11:1081644::G 9615/126540)
Row 132380 (NC_000001.11:1081644::GG 113/126770)
Row 132381 (NC_000001.11:1081644::GGG 19/126764)...

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

Submission ignored due to conflicting rows:
Row 132379 (NC_000001.11:1081644::G 9615/126540)
Row 132380 (NC_000001.11:1081644::GG 113/126770)
Row 132381 (NC_000001.11:1081644::GGG 19/126764)...

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

Submission ignored due to conflicting rows:
Row 132379 (NC_000001.11:1081644::G 9615/126540)
Row 132380 (NC_000001.11:1081644::GG 113/126770)
Row 132381 (NC_000001.11:1081644::GGG 19/126764)...

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

Submission ignored due to conflicting rows:
Row 132379 (NC_000001.11:1081644::G 9615/126540)
Row 132380 (NC_000001.11:1081644::GG 113/126770)
Row 132381 (NC_000001.11:1081644::GGG 19/126764)...

- Apr 25, 2021 (155)
38 Korean Genome Project NC_000001.11 - 1081645 Apr 25, 2020 (154)
39 Northern Sweden NC_000001.10 - 1017025 Jul 12, 2019 (153)
40 8.3KJPN

Submission ignored due to conflicting rows:
Row 34522 (NC_000001.10:1017024::G 728/16676)
Row 34523 (NC_000001.10:1017024::GG 3/16676)

- Apr 25, 2021 (155)
41 8.3KJPN

Submission ignored due to conflicting rows:
Row 34522 (NC_000001.10:1017024::G 728/16676)
Row 34523 (NC_000001.10:1017024::GG 3/16676)

- Apr 25, 2021 (155)
42 UK 10K study - Twins

Submission ignored due to conflicting rows:
Row 4191 (NC_000001.10:1017024:G: 363/3708)
Row 4192 (NC_000001.10:1017024::G 139/3708)

- Oct 11, 2018 (152)
43 UK 10K study - Twins

Submission ignored due to conflicting rows:
Row 4191 (NC_000001.10:1017024:G: 363/3708)
Row 4192 (NC_000001.10:1017024::G 139/3708)

- Oct 11, 2018 (152)
44 ALFA NC_000001.11 - 1081645 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)
rs143553062 Sep 17, 2011 (135)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss1700145909, ss1700154876 NC_000001.10:1017024:G: NC_000001.11:1081644:GGGG:GGG (self)
ss325997312, ss550899271 NC_000001.9:1006887::G NC_000001.11:1081644:GGGG:GGGGG (self)
3126, 3272, ss498763980, ss2986153778, ss3654264878, ss3726718407, ss3783302995, ss3788980782, ss3793853331, ss3825982463, ss5142065215 NC_000001.10:1017024::G NC_000001.11:1081644:GGGG:GGGGG (self)
ss1709905415, ss1709907376 NC_000001.10:1017025::G NC_000001.11:1081644:GGGG:GGGGG (self)
13435, ss3066463475, ss3685997261, ss3943635434, ss3986964738 NC_000001.11:1081644::G NC_000001.11:1081644:GGGG:GGGGG (self)
10821702288 NC_000001.11:1081644:GGGG:GGGGG NC_000001.11:1081644:GGGG:GGGGG
ss193082067 NT_032977.10:495656::G NC_000001.11:1081644:GGGG:GGGGG (self)
ss3788980783, ss3793853332, ss5142065216 NC_000001.10:1017024::GG NC_000001.11:1081644:GGGG:GGGGGG (self)
ss3066463476, ss3685997260, ss3986964739 NC_000001.11:1081644::GG NC_000001.11:1081644:GGGG:GGGGGG (self)
10821702288 NC_000001.11:1081644:GGGG:GGGGGG NC_000001.11:1081644:GGGG:GGGGGG
ss3066463477, ss3685997259, ss3986964740 NC_000001.11:1081644::GGG NC_000001.11:1081644:GGGG:GGGGGGG (self)
10821702288 NC_000001.11:1081644:GGGG:GGGGGGG NC_000001.11:1081644:GGGG:GGGGGGG
ss3986964741 NC_000001.11:1081644::GGGG NC_000001.11:1081644:GGGG:GGGGGGGG
10821702288 NC_000001.11:1081644:GGGG:GGGGGGGG NC_000001.11:1081644:GGGG:GGGGGGGG
Removed from this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Destination RSIDs
NC_000001.10:1017024::GGG NC_000001.11:1081644:GGGG:GGGGGGG
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 rs113385670

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