Name: rs144685080
Published: September 21, 2022
License: Open Access

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 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:902950-902953 (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: dupC
Variation Type: Indel Insertion and Deletion
Frequency: dupC=0.167502 (44336/264690, TOPMED)
dupC=0.174052 (24370/140016, GnomAD)
dupC=0.24727 (6985/28248, 14KJPN) (+ 11 more)
dupC=0.18656 (3455/18520, ALFA)
dupC=0.24442 (4093/16746, 8.3KJPN)
dupC=0.1669 (1069/6404, 1000G_30x)
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: LOC284600 : 2KB Upstream 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: 20230706150541

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

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").

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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
14KJPN	JAPANESE	Study-wide	28248	- No frequency provided	dupC=0.24727
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_30x	Global	Study-wide	6404	- No frequency provided	dupC=0.1669
1000Genomes_30x	African	Sub	1786	- No frequency provided	dupC=0.0773
1000Genomes_30x	Europe	Sub	1266	- No frequency provided	dupC=0.1983
1000Genomes_30x	South Asian	Sub	1202	- No frequency provided	dupC=0.2296
1000Genomes_30x	East Asian	Sub	1170	- No frequency provided	dupC=0.1684
1000Genomes_30x	American	Sub	980	- No frequency provided	dupC=0.211
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

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 1	NC_000001.11:g.902953dup
GRCh37.p13 chr 1	NC_000001.10:g.838333dup

Gene: LOC284600, uncharacterized LOC284600 (plus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
LOC284600 transcript variant X2	XR_007065341.1:n.	N/A	Upstream Transcript Variant
LOC284600 transcript variant X5	XR_007065344.1:n.	N/A	Upstream Transcript Variant
LOC284600 transcript variant X7	XR_007065346.1:n.	N/A	Upstream Transcript Variant
LOC284600 transcript variant X1	XR_007065340.1:n.	N/A	N/A
LOC284600 transcript variant X3	XR_007065342.1:n.	N/A	N/A
LOC284600 transcript variant X4	XR_007065343.1:n.	N/A	N/A
LOC284600 transcript variant X6	XR_007065345.1:n.	N/A	N/A
LOC284600 transcript variant X8	XR_007065347.1:n.	N/A	N/A

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

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.p14 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

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#.

36 SubSNP, 14 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	GNOMAD	ss2750646154	Nov 08, 2017 (151)
15	SWEGEN	ss2986150621	Nov 08, 2017 (151)
16	MCHAISSO	ss3064386054	Nov 08, 2017 (151)
17	MCHAISSO	ss3065282528	Nov 08, 2017 (151)
18	BIOINF_KMB_FNS_UNIBA	ss3645022424	Oct 11, 2018 (152)
19	EGCUT_WGS	ss3654261828	Jul 12, 2019 (153)
20	EVA_DECODE	ss3685993053	Jul 12, 2019 (153)
21	ACPOP	ss3726716755	Jul 12, 2019 (153)
22	KHV_HUMAN_GENOMES	ss3798744250	Jul 12, 2019 (153)
23	EVA	ss3825981624	Apr 25, 2020 (154)
24	KOGIC	ss3943630907	Apr 25, 2020 (154)
25	TOPMED	ss4436448877	Apr 25, 2021 (155)
26	TOMMO_GENOMICS	ss5142055427	Apr 25, 2021 (155)
27	1000G_HIGH_COVERAGE	ss5240865445	Oct 12, 2022 (156)
28	HUGCELL_USP	ss5442113394	Oct 12, 2022 (156)
29	1000G_HIGH_COVERAGE	ss5512490912	Oct 12, 2022 (156)
30	SANFORD_IMAGENETICS	ss5624750898	Oct 12, 2022 (156)
31	TOMMO_GENOMICS	ss5666195770	Oct 12, 2022 (156)
32	YY_MCH	ss5800244371	Oct 12, 2022 (156)
33	EVA	ss5831419319	Oct 12, 2022 (156)
34	EVA	ss5848748986	Oct 12, 2022 (156)
35	EVA	ss5906706201	Oct 12, 2022 (156)
36	EVA	ss5936583546	Oct 12, 2022 (156)
37	1000Genomes	NC_000001.10 - 838330	Oct 11, 2018 (152)
38	1000Genomes_30x	NC_000001.11 - 902950	Oct 12, 2022 (156)
39	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 838330	Oct 11, 2018 (152)
40	Genetic variation in the Estonian population	NC_000001.10 - 838330	Oct 11, 2018 (152)
41	The Danish reference pan genome	NC_000001.10 - 838330	Apr 25, 2020 (154)
42	gnomAD - Genomes	NC_000001.11 - 902950	Apr 25, 2021 (155)
43	Korean Genome Project	NC_000001.11 - 902950	Apr 25, 2020 (154)
44	Northern Sweden	NC_000001.10 - 838330	Jul 12, 2019 (153)
45	8.3KJPN	NC_000001.10 - 838330	Apr 25, 2021 (155)
46	14KJPN	NC_000001.11 - 902950	Oct 12, 2022 (156)
47	TopMed	NC_000001.11 - 902950	Apr 25, 2021 (155)
48	UK 10K study - Twins	NC_000001.10 - 838330	Oct 11, 2018 (152)
49	A Vietnamese Genetic Variation Database	NC_000001.10 - 838330	Jul 12, 2019 (153)
50	ALFA	NC_000001.11 - 902950	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)
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, ss2750646154, ss2986150621, ss3654261828, ss3726716755, ss3825981624, ss5142055427, ss5624750898, ss5831419319, ss5936583546	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)
16847, 79172, 8908, 32874, 55212, ss3064386054, ss3065282528, ss3645022424, ss3685993053, ss3798744250, ss3943630907, ss4436448877, ss5240865445, ss5442113394, ss5512490912, ss5666195770, ss5800244371, ss5848748986, ss5906706201	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)

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

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs144685080