Name: rs2980295
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.

rs2980295

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:847924 (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: T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.026253 (6949/264690, TOPMED)
T=0.024124 (3379/140070, GnomAD)
T=0.00916 (275/30018, ALFA) (+ 10 more)
T=0.00000 (0/28258, 14KJPN)
T=0.00000 (0/16760, 8.3KJPN)
T=0.0220 (141/6404, 1000G_30x)
T=0.0206 (103/5008, 1000G)
T=0.0000 (0/2928, KOREAN)
T=0.0000 (0/1832, Korea1K)
T=0.000 (0/600, NorthernSweden)
T=0.004 (2/558, SGDP_PRJ)
T=0.009 (2/216, Qatari)
T=0.00 (0/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LINC01128 : Intron 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	30018	T=0.00916	C=0.99084
European	Sub	24604	T=0.00110	C=0.99890
African	Sub	3138	T=0.0707	C=0.9293
African Others	Sub	124	T=0.129	C=0.871
African American	Sub	3014	T=0.0683	C=0.9317
Asian	Sub	126	T=0.000	C=1.000
East Asian	Sub	98	T=0.00	C=1.00
Other Asian	Sub	28	T=0.00	C=1.00
Latin American 1	Sub	164	T=0.037	C=0.963
Latin American 2	Sub	684	T=0.012	C=0.988
South Asian	Sub	114	T=0.000	C=1.000
Other	Sub	1188	T=0.0101	C=0.9899

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	T=0.026253	C=0.973747
gnomAD - Genomes	Global	Study-wide	140070	T=0.024124	C=0.975876
gnomAD - Genomes	European	Sub	75904	T=0.00148	C=0.99852
gnomAD - Genomes	African	Sub	41918	T=0.07317	C=0.92683
gnomAD - Genomes	American	Sub	13644	T=0.01092	C=0.98908
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.0021	C=0.9979
gnomAD - Genomes	East Asian	Sub	3134	T=0.0000	C=1.0000
gnomAD - Genomes	Other	Sub	2146	T=0.0205	C=0.9795
Allele Frequency Aggregator	Total	Global	30018	T=0.00916	C=0.99084
Allele Frequency Aggregator	European	Sub	24604	T=0.00110	C=0.99890
Allele Frequency Aggregator	African	Sub	3138	T=0.0707	C=0.9293
Allele Frequency Aggregator	Other	Sub	1188	T=0.0101	C=0.9899
Allele Frequency Aggregator	Latin American 2	Sub	684	T=0.012	C=0.988
Allele Frequency Aggregator	Latin American 1	Sub	164	T=0.037	C=0.963
Allele Frequency Aggregator	Asian	Sub	126	T=0.000	C=1.000
Allele Frequency Aggregator	South Asian	Sub	114	T=0.000	C=1.000
14KJPN	JAPANESE	Study-wide	28258	T=0.00000	C=1.00000
8.3KJPN	JAPANESE	Study-wide	16760	T=0.00000	C=1.00000
1000Genomes_30x	Global	Study-wide	6404	T=0.0220	C=0.9780
1000Genomes_30x	African	Sub	1786	T=0.0705	C=0.9295
1000Genomes_30x	Europe	Sub	1266	T=0.0055	C=0.9945
1000Genomes_30x	South Asian	Sub	1202	T=0.0000	C=1.0000
1000Genomes_30x	East Asian	Sub	1170	T=0.0000	C=1.0000
1000Genomes_30x	American	Sub	980	T=0.008	C=0.992
1000Genomes	Global	Study-wide	5008	T=0.0206	C=0.9794
1000Genomes	African	Sub	1322	T=0.0696	C=0.9304
1000Genomes	East Asian	Sub	1008	T=0.0000	C=1.0000
1000Genomes	Europe	Sub	1006	T=0.0050	C=0.9950
1000Genomes	South Asian	Sub	978	T=0.000	C=1.000
1000Genomes	American	Sub	694	T=0.009	C=0.991
KOREAN population from KRGDB	KOREAN	Study-wide	2928	T=0.0000	C=1.0000
Korean Genome Project	KOREAN	Study-wide	1832	T=0.0000	C=1.0000
Northern Sweden	ACPOP	Study-wide	600	T=0.000	C=1.000
SGDP_PRJ	Global	Study-wide	558	T=0.004	C=0.996
Qatari	Global	Study-wide	216	T=0.009	C=0.991
The Danish reference pan genome	Danish	Study-wide	40	T=0.00	C=1.00

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.847924T>C
GRCh37.p13 chr 1	NC_000001.10:g.783304T>C

Gene: LINC01128, long intergenic non-protein coding RNA 1128 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC01128 transcript variant 1	NR_047519.1:n.	N/A	Intron Variant
LINC01128 transcript variant 3	NR_047521.1:n.	N/A	Intron Variant
LINC01128 transcript variant 5	NR_047523.1:n.	N/A	Intron Variant
LINC01128 transcript variant 7	NR_047524.1:n.	N/A	Intron Variant
LINC01128 transcript variant 8	NR_047525.1:n.	N/A	Intron Variant
LINC01128 transcript variant 9	NR_047526.1:n.	N/A	Genic Downstream Transcript 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

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=	C
GRCh38.p14 chr 1	NC_000001.11:g.847924=	NC_000001.11:g.847924T>C
GRCh37.p13 chr 1	NC_000001.10:g.783304=	NC_000001.10:g.783304T>C

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#.

66 SubSNP, 13 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss4194504	Nov 05, 2001 (101)
2	BCM_SSAHASNP	ss9876058	Jul 11, 2003 (117)
3	CSHL-HAPMAP	ss16411266	Feb 27, 2004 (120)
4	CSHL-HAPMAP	ss17343075	Feb 27, 2004 (120)
5	SSAHASNP	ss20499842	Apr 05, 2004 (121)
6	HGSV	ss77564109	Dec 06, 2007 (129)
7	HGSV	ss80082473	Dec 15, 2007 (130)
8	HGSV	ss85518833	Dec 15, 2007 (130)
9	BCMHGSC_JDW	ss87155962	Mar 23, 2008 (129)
10	HUMANGENOME_JCVI	ss97913237	Feb 05, 2009 (130)
11	BGI	ss105111707	Dec 01, 2009 (147)
12	ILLUMINA-UK	ss118438358	Feb 14, 2009 (130)
13	ENSEMBL	ss138892361	Dec 01, 2009 (147)
14	GMI	ss154522404	Dec 01, 2009 (147)
15	BCM-HGSC-SUB	ss205532692	Jul 04, 2010 (132)
16	BL	ss252864166	May 09, 2011 (134)
17	GMI	ss275680890	May 04, 2012 (137)
18	GMI	ss283987403	Apr 25, 2013 (138)
19	PJP	ss290493810	May 09, 2011 (134)
20	1000GENOMES	ss328357811	May 09, 2011 (134)
21	ILLUMINA	ss479945029	May 04, 2012 (137)
22	ILLUMINA	ss482404406	May 04, 2012 (137)
23	ILLUMINA	ss533414063	Sep 08, 2015 (146)
24	TISHKOFF	ss553710562	Apr 25, 2013 (138)
25	SSMP	ss647516303	Apr 25, 2013 (138)
26	ILLUMINA	ss779171954	Aug 21, 2014 (142)
27	ILLUMINA	ss781107896	Aug 21, 2014 (142)
28	ILLUMINA	ss834637138	Aug 21, 2014 (142)
29	1000GENOMES	ss1289339758	Aug 21, 2014 (142)
30	DDI	ss1425684892	Apr 01, 2015 (144)
31	EVA_GENOME_DK	ss1573851181	Apr 01, 2015 (144)
32	HAMMER_LAB	ss1793705967	Sep 08, 2015 (146)
33	WEILL_CORNELL_DGM	ss1917960551	Feb 12, 2016 (147)
34	SYSTEMSBIOZJU	ss2624264795	Nov 08, 2017 (151)
35	ILLUMINA	ss2632465455	Nov 08, 2017 (151)
36	GRF	ss2697374735	Nov 08, 2017 (151)
37	GNOMAD	ss2750640005	Nov 08, 2017 (151)
38	SWEGEN	ss2986149226	Nov 08, 2017 (151)
39	CSHL	ss3343272625	Nov 08, 2017 (151)
40	ILLUMINA	ss3626006518	Oct 11, 2018 (152)
41	ILLUMINA	ss3630505580	Oct 11, 2018 (152)
42	OMUKHERJEE_ADBS	ss3646218693	Oct 11, 2018 (152)
43	URBANLAB	ss3646581235	Oct 11, 2018 (152)
44	ACPOP	ss3726716435	Jul 12, 2019 (153)
45	PACBIO	ss3783302165	Jul 12, 2019 (153)
46	PACBIO	ss3788980030	Jul 12, 2019 (153)
47	PACBIO	ss3793852566	Jul 12, 2019 (153)
48	KHV_HUMAN_GENOMES	ss3798743725	Jul 12, 2019 (153)
49	EVA	ss3825981484	Apr 25, 2020 (154)
50	EVA	ss3836378436	Apr 25, 2020 (154)
51	EVA	ss3841782436	Apr 25, 2020 (154)
52	SGDP_PRJ	ss3847995758	Apr 25, 2020 (154)
53	KRGDB	ss3892836041	Apr 25, 2020 (154)
54	KOGIC	ss3943629805	Apr 25, 2020 (154)
55	TOPMED	ss4436436299	Apr 25, 2021 (155)
56	TOMMO_GENOMICS	ss5142052621	Apr 25, 2021 (155)
57	1000G_HIGH_COVERAGE	ss5240863812	Oct 12, 2022 (156)
58	EVA	ss5316183924	Oct 12, 2022 (156)
59	1000G_HIGH_COVERAGE	ss5512488605	Oct 12, 2022 (156)
60	SANFORD_IMAGENETICS	ss5624749557	Oct 12, 2022 (156)
61	TOMMO_GENOMICS	ss5666192036	Oct 12, 2022 (156)
62	YY_MCH	ss5800243838	Oct 12, 2022 (156)
63	EVA	ss5831418505	Oct 12, 2022 (156)
64	EVA	ss5848748889	Oct 12, 2022 (156)
65	EVA	ss5906704978	Oct 12, 2022 (156)
66	EVA	ss5936582822	Oct 12, 2022 (156)
67	1000Genomes	NC_000001.10 - 783304	Oct 11, 2018 (152)
68	1000Genomes_30x	NC_000001.11 - 847924	Oct 12, 2022 (156)
69	The Danish reference pan genome	NC_000001.10 - 783304	Apr 25, 2020 (154)
70	gnomAD - Genomes	NC_000001.11 - 847924	Apr 25, 2021 (155)
71	KOREAN population from KRGDB	NC_000001.10 - 783304	Apr 25, 2020 (154)
72	Korean Genome Project	NC_000001.11 - 847924	Apr 25, 2020 (154)
73	Northern Sweden	NC_000001.10 - 783304	Jul 12, 2019 (153)
74	Qatari	NC_000001.10 - 783304	Apr 25, 2020 (154)
75	SGDP_PRJ	NC_000001.10 - 783304	Apr 25, 2020 (154)
76	8.3KJPN	NC_000001.10 - 783304	Apr 25, 2021 (155)
77	14KJPN	NC_000001.11 - 847924	Oct 12, 2022 (156)
78	TopMed	NC_000001.11 - 847924	Apr 25, 2021 (155)
79	ALFA	NC_000001.11 - 847924	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)
rs6689637	Aug 27, 2003 (117)
rs58810853	May 24, 2008 (130)
rs75216674	Jul 19, 2016 (147)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss77564109, ss80082473, ss85518833	NC_000001.8:823166:T:C	NC_000001.11:847923:T:C	(self)
ss87155962, ss118438358, ss205532692, ss252864166, ss275680890, ss283987403, ss290493810, ss482404406	NC_000001.9:773166:T:C	NC_000001.11:847923:T:C	(self)
4502, 1358415, 13435, 1300, 2481, 12738, 21928, ss328357811, ss479945029, ss533414063, ss553710562, ss647516303, ss779171954, ss781107896, ss834637138, ss1289339758, ss1425684892, ss1573851181, ss1793705967, ss1917960551, ss2624264795, ss2632465455, ss2697374735, ss2750640005, ss2986149226, ss3343272625, ss3626006518, ss3630505580, ss3646218693, ss3726716435, ss3783302165, ss3788980030, ss3793852566, ss3825981484, ss3836378436, ss3847995758, ss3892836041, ss5142052621, ss5316183924, ss5624749557, ss5831418505, ss5936582822	NC_000001.10:783303:T:C	NC_000001.11:847923:T:C	(self)
14540, 67938, 7806, 29140, 42634, 14509644547, ss3646581235, ss3798743725, ss3841782436, ss3943629805, ss4436436299, ss5240863812, ss5512488605, ss5666192036, ss5800243838, ss5848748889, ss5906704978	NC_000001.11:847923:T:C	NC_000001.11:847923:T:C	(self)
ss4194504, ss97913237, ss105111707, ss138892361, ss154522404	NT_004350.19:261935:T:C	NC_000001.11:847923:T:C	(self)
ss9876058, ss16411266, ss17343075, ss20499842	NT_034471.3:261935:T:C	NC_000001.11:847923:T:C	(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 rs2980295

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

rs2980295