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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.

rs144685080

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:902950-902953 (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
dupC
Variation Type
Indel Insertion and Deletion
Frequency
dupC=0.167502 (44336/264690, TOPMED)
dupC=0.174052 (24370/140016, GnomAD)
dupC=0.18656 (3455/18520, ALFA) (+ 9 more)
dupC=0.24442 (4093/16746, 8.3KJPN)
dupC=0.1723 (863/5008, 1000G)
dupC=0.1946 (872/4480, Estonian)
dupC=0.2130 (821/3854, ALSPAC)
dupC=0.2136 (792/3708, TWINSUK)
dupC=0.1559 (285/1828, Korea1K)
dupC=0.175 (105/600, NorthernSweden)
dupC=0.187 (40/214, Vietnamese)
dupC=0.23 (9/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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.902953dup
GRCh37.p13 chr 1 NC_000001.10:g.838333dup
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 18520 CCCC=0.81344 CCCCC=0.18656
European Sub 14152 CCCC=0.79353 CCCCC=0.20647
African Sub 2898 CCCC=0.9168 CCCCC=0.0832
African Others Sub 114 CCCC=0.930 CCCCC=0.070
African American Sub 2784 CCCC=0.9163 CCCCC=0.0837
Asian Sub 112 CCCC=0.866 CCCCC=0.134
East Asian Sub 86 CCCC=0.88 CCCCC=0.12
Other Asian Sub 26 CCCC=0.81 CCCCC=0.19
Latin American 1 Sub 146 CCCC=0.801 CCCCC=0.199
Latin American 2 Sub 610 CCCC=0.782 CCCCC=0.218
South Asian Sub 98 CCCC=0.78 CCCCC=0.22
Other Sub 504 CCCC=0.815 CCCCC=0.185


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 -

No frequency provided

dupC=0.167502
gnomAD - Genomes Global Study-wide 140016 -

No frequency provided

dupC=0.174052
gnomAD - Genomes European Sub 75798 -

No frequency provided

dupC=0.21402
gnomAD - Genomes African Sub 41980 -

No frequency provided

dupC=0.09052
gnomAD - Genomes American Sub 13642 -

No frequency provided

dupC=0.19667
gnomAD - Genomes Ashkenazi Jewish Sub 3318 -

No frequency provided

dupC=0.2679
gnomAD - Genomes East Asian Sub 3128 -

No frequency provided

dupC=0.1266
gnomAD - Genomes Other Sub 2150 -

No frequency provided

dupC=0.1767
Allele Frequency Aggregator Total Global 18520 (C)4=0.81344 dupC=0.18656
Allele Frequency Aggregator European Sub 14152 (C)4=0.79353 dupC=0.20647
Allele Frequency Aggregator African Sub 2898 (C)4=0.9168 dupC=0.0832
Allele Frequency Aggregator Latin American 2 Sub 610 (C)4=0.782 dupC=0.218
Allele Frequency Aggregator Other Sub 504 (C)4=0.815 dupC=0.185
Allele Frequency Aggregator Latin American 1 Sub 146 (C)4=0.801 dupC=0.199
Allele Frequency Aggregator Asian Sub 112 (C)4=0.866 dupC=0.134
Allele Frequency Aggregator South Asian Sub 98 (C)4=0.78 dupC=0.22
8.3KJPN JAPANESE Study-wide 16746 -

No frequency provided

dupC=0.24442
1000Genomes Global Study-wide 5008 -

No frequency provided

dupC=0.1723
1000Genomes African Sub 1322 -

No frequency provided

dupC=0.0779
1000Genomes East Asian Sub 1008 -

No frequency provided

dupC=0.1736
1000Genomes Europe Sub 1006 -

No frequency provided

dupC=0.2087
1000Genomes South Asian Sub 978 -

No frequency provided

dupC=0.237
1000Genomes American Sub 694 -

No frequency provided

dupC=0.206
Genetic variation in the Estonian population Estonian Study-wide 4480 -

No frequency provided

dupC=0.1946
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 -

No frequency provided

dupC=0.2130
UK 10K study - Twins TWIN COHORT Study-wide 3708 -

No frequency provided

dupC=0.2136
Korean Genome Project KOREAN Study-wide 1828 -

No frequency provided

dupC=0.1559
Northern Sweden ACPOP Study-wide 600 -

No frequency provided

dupC=0.175
A Vietnamese Genetic Variation Database Global Study-wide 214 -

No frequency provided

dupC=0.187
The Danish reference pan genome Danish Study-wide 40 -

No frequency provided

dupC=0.23
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 (C)4= dupC
GRCh38.p13 chr 1 NC_000001.11:g.902950_902953= NC_000001.11:g.902953dup
GRCh37.p13 chr 1 NC_000001.10:g.838330_838333= NC_000001.10:g.838333dup
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#.

28 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss325997516 May 09, 2011 (134)
2 1000GENOMES ss498763866 May 04, 2012 (137)
3 LUNTER ss550899155 Apr 25, 2013 (138)
4 LUNTER ss550903140 Apr 25, 2013 (138)
5 LUNTER ss552739032 Apr 25, 2013 (138)
6 TISHKOFF ss553745542 Apr 25, 2013 (138)
7 SSMP ss663209701 Apr 01, 2015 (144)
8 EVA-GONL ss974769908 Aug 21, 2014 (142)
9 1000GENOMES ss1367645479 Aug 21, 2014 (142)
10 EVA_GENOME_DK ss1573868313 Apr 01, 2015 (144)
11 EVA_UK10K_ALSPAC ss1700143237 Apr 01, 2015 (144)
12 EVA_UK10K_TWINSUK ss1700153792 Apr 01, 2015 (144)
13 JJLAB ss2030297762 Sep 14, 2016 (149)
14 TOPMED ss2321507267 Dec 20, 2016 (150)
15 GNOMAD ss2750646154 Nov 08, 2017 (151)
16 SWEGEN ss2986150621 Nov 08, 2017 (151)
17 MCHAISSO ss3064386054 Nov 08, 2017 (151)
18 MCHAISSO ss3065282528 Nov 08, 2017 (151)
19 TOPMED ss3066414040 Nov 08, 2017 (151)
20 BIOINF_KMB_FNS_UNIBA ss3645022424 Oct 11, 2018 (152)
21 EGCUT_WGS ss3654261828 Jul 12, 2019 (153)
22 EVA_DECODE ss3685993053 Jul 12, 2019 (153)
23 ACPOP ss3726716755 Jul 12, 2019 (153)
24 KHV_HUMAN_GENOMES ss3798744250 Jul 12, 2019 (153)
25 EVA ss3825981624 Apr 25, 2020 (154)
26 KOGIC ss3943630907 Apr 25, 2020 (154)
27 TOPMED ss4436448877 Apr 25, 2021 (155)
28 TOMMO_GENOMICS ss5142055427 Apr 25, 2021 (155)
29 1000Genomes NC_000001.10 - 838330 Oct 11, 2018 (152)
30 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 838330 Oct 11, 2018 (152)
31 Genetic variation in the Estonian population NC_000001.10 - 838330 Oct 11, 2018 (152)
32 The Danish reference pan genome NC_000001.10 - 838330 Apr 25, 2020 (154)
33 gnomAD - Genomes NC_000001.11 - 902950 Apr 25, 2021 (155)
34 Korean Genome Project NC_000001.11 - 902950 Apr 25, 2020 (154)
35 Northern Sweden NC_000001.10 - 838330 Jul 12, 2019 (153)
36 8.3KJPN NC_000001.10 - 838330 Apr 25, 2021 (155)
37 TopMed NC_000001.11 - 902950 Apr 25, 2021 (155)
38 UK 10K study - Twins NC_000001.10 - 838330 Oct 11, 2018 (152)
39 A Vietnamese Genetic Variation Database NC_000001.10 - 838330 Jul 12, 2019 (153)
40 ALFA NC_000001.11 - 902950 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)
rs369533606 May 15, 2013 (138)
rs371825888 May 15, 2013 (138)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss325997516, ss550899155, ss550903140, ss552739032 NC_000001.9:828192::C NC_000001.11:902949:CCCC:CCCCC (self)
6226, 911, 76, 120269, 1620, 24734, 911, 189, ss498763866, ss663209701, ss974769908, ss1367645479, ss1573868313, ss1700143237, ss1700153792, ss2030297762, ss2321507267, ss2750646154, ss2986150621, ss3654261828, ss3726716755, ss3825981624, ss5142055427 NC_000001.10:838329::C NC_000001.11:902949:CCCC:CCCCC (self)
ss553745542 NC_000001.10:838333::C NC_000001.11:902949:CCCC:CCCCC (self)
79172, 8908, 26686, 55212, ss3064386054, ss3065282528, ss3066414040, ss3645022424, ss3685993053, ss3798744250, ss3943630907, ss4436448877 NC_000001.11:902949::C NC_000001.11:902949:CCCC:CCCCC (self)
1644057869 NC_000001.11:902949:CCCC:CCCCC NC_000001.11:902949:CCCC:CCCCC (self)
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 rs144685080

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