Name: rs2980300
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.

rs2980300

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:850609 (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>A / T>C / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.354781 (93907/264690, TOPMED)
T=0.343393 (48075/140000, GnomAD)
T=0.27711 (14430/52074, ALFA) (+ 14 more)
T=0.38587 (10904/28258, 14KJPN)
T=0.38305 (6420/16760, 8.3KJPN)
T=0.3854 (2468/6404, 1000G_30x)
T=0.3730 (1868/5008, 1000G)
T=0.1258 (485/3854, ALSPAC)
T=0.1324 (491/3708, TWINSUK)
T=0.3232 (947/2930, KOREAN)
T=0.4711 (830/1762, HapMap)
T=0.145 (145/998, GoNL)
T=0.135 (81/600, NorthernSweden)
T=0.222 (101/454, SGDP_PRJ)
T=0.315 (68/216, Qatari)
T=0.17 (9/52, Siberian)
T=0.03 (1/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LINC01128 : Intron Variant
Publications: 1 citation
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	52074	T=0.27711	A=0.00000, C=0.72289
European	Sub	32348	T=0.15250	A=0.00000, C=0.84750
African	Sub	8276	T=0.7819	A=0.0000, C=0.2181
African Others	Sub	286	T=0.906	A=0.000, C=0.094
African American	Sub	7990	T=0.7775	A=0.0000, C=0.2225
Asian	Sub	386	T=0.285	A=0.000, C=0.715
East Asian	Sub	312	T=0.324	A=0.000, C=0.676
Other Asian	Sub	74	T=0.12	A=0.00, C=0.88
Latin American 1	Sub	612	T=0.345	A=0.000, C=0.655
Latin American 2	Sub	6500	T=0.2865	A=0.0000, C=0.7135
South Asian	Sub	80	T=0.25	A=0.00, C=0.75
Other	Sub	3872	T=0.2126	A=0.0000, C=0.7874

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=0.354781	C=0.645219
gnomAD - Genomes	Global	Study-wide	140000	T=0.343393	C=0.656607
gnomAD - Genomes	European	Sub	75842	T=0.15234	C=0.84766
gnomAD - Genomes	African	Sub	41924	T=0.73512	C=0.26488
gnomAD - Genomes	American	Sub	13648	T=0.27257	C=0.72743
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=0.1611	C=0.8389
gnomAD - Genomes	East Asian	Sub	3122	T=0.2530	C=0.7470
gnomAD - Genomes	Other	Sub	2144	T=0.3064	C=0.6936
Allele Frequency Aggregator	Total	Global	52074	T=0.27711	A=0.00000, C=0.72289
Allele Frequency Aggregator	European	Sub	32348	T=0.15250	A=0.00000, C=0.84750
Allele Frequency Aggregator	African	Sub	8276	T=0.7819	A=0.0000, C=0.2181
Allele Frequency Aggregator	Latin American 2	Sub	6500	T=0.2865	A=0.0000, C=0.7135
Allele Frequency Aggregator	Other	Sub	3872	T=0.2126	A=0.0000, C=0.7874
Allele Frequency Aggregator	Latin American 1	Sub	612	T=0.345	A=0.000, C=0.655
Allele Frequency Aggregator	Asian	Sub	386	T=0.285	A=0.000, C=0.715
Allele Frequency Aggregator	South Asian	Sub	80	T=0.25	A=0.00, C=0.75
14KJPN	JAPANESE	Study-wide	28258	T=0.38587	C=0.61413
8.3KJPN	JAPANESE	Study-wide	16760	T=0.38305	C=0.61695
1000Genomes_30x	Global	Study-wide	6404	T=0.3854	C=0.6146
1000Genomes_30x	African	Sub	1786	T=0.8421	C=0.1579
1000Genomes_30x	Europe	Sub	1266	T=0.1232	C=0.8768
1000Genomes_30x	South Asian	Sub	1202	T=0.2063	C=0.7937
1000Genomes_30x	East Asian	Sub	1170	T=0.2632	C=0.7368
1000Genomes_30x	American	Sub	980	T=0.257	C=0.743
1000Genomes	Global	Study-wide	5008	T=0.3730	C=0.6270
1000Genomes	African	Sub	1322	T=0.8313	C=0.1687
1000Genomes	East Asian	Sub	1008	T=0.2639	C=0.7361
1000Genomes	Europe	Sub	1006	T=0.1272	C=0.8728
1000Genomes	South Asian	Sub	978	T=0.204	C=0.796
1000Genomes	American	Sub	694	T=0.252	C=0.748
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.1258	C=0.8742
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.1324	C=0.8676
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.3232	A=0.0000, C=0.6768, G=0.0000
HapMap	Global	Study-wide	1762	T=0.4711	C=0.5289
HapMap	African	Sub	686	T=0.838	C=0.162
HapMap	American	Sub	654	T=0.260	C=0.740
HapMap	Asian	Sub	246	T=0.285	C=0.715
HapMap	Europe	Sub	176	T=0.085	C=0.915
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.145	C=0.855
Northern Sweden	ACPOP	Study-wide	600	T=0.135	C=0.865
SGDP_PRJ	Global	Study-wide	454	T=0.222	C=0.778
Qatari	Global	Study-wide	216	T=0.315	C=0.685
Siberian	Global	Study-wide	52	T=0.17	C=0.83
The Danish reference pan genome	Danish	Study-wide	40	T=0.03	C=0.97

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.850609T>A
GRCh38.p14 chr 1	NC_000001.11:g.850609T>C
GRCh38.p14 chr 1	NC_000001.11:g.850609T>G
GRCh37.p13 chr 1	NC_000001.10:g.785989T>A
GRCh37.p13 chr 1	NC_000001.10:g.785989T>C
GRCh37.p13 chr 1	NC_000001.10:g.785989T>G

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=	A	C	G
GRCh38.p14 chr 1	NC_000001.11:g.850609=	NC_000001.11:g.850609T>A	NC_000001.11:g.850609T>C	NC_000001.11:g.850609T>G
GRCh37.p13 chr 1	NC_000001.10:g.785989=	NC_000001.10:g.785989T>A	NC_000001.10:g.785989T>C	NC_000001.10:g.785989T>G

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#.

82 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss4194509	Nov 05, 2001 (101)
2	SSAHASNP	ss20575722	Apr 05, 2004 (121)
3	ABI	ss41187782	Mar 13, 2006 (126)
4	AFFY	ss66317030	Dec 01, 2006 (127)
5	ILLUMINA	ss75264617	Dec 06, 2007 (129)
6	AFFY	ss76002276	Dec 06, 2007 (129)
7	KRIBB_YJKIM	ss81922362	Dec 14, 2007 (130)
8	BCMHGSC_JDW	ss87155983	Mar 23, 2008 (129)
9	HUMANGENOME_JCVI	ss97913239	Feb 06, 2009 (130)
10	BGI	ss105111712	Feb 23, 2009 (131)
11	1000GENOMES	ss107938285	Jan 22, 2009 (130)
12	1000GENOMES	ss109937332	Jan 24, 2009 (130)
13	ILLUMINA-UK	ss118438368	Feb 14, 2009 (130)
14	ENSEMBL	ss137752300	Dec 01, 2009 (131)
15	ENSEMBL	ss138891772	Dec 01, 2009 (131)
16	GMI	ss154522410	Dec 01, 2009 (131)
17	ILLUMINA	ss160604319	Dec 01, 2009 (131)
18	COMPLETE_GENOMICS	ss162980873	Jul 04, 2010 (132)
19	AFFY	ss170255113	Jul 04, 2010 (132)
20	ILLUMINA	ss173546293	Jul 04, 2010 (132)
21	BUSHMAN	ss197885475	Jul 04, 2010 (132)
22	BCM-HGSC-SUB	ss205120721	Jul 04, 2010 (132)
23	1000GENOMES	ss218190445	Jul 14, 2010 (132)
24	1000GENOMES	ss230395484	Jul 14, 2010 (132)
25	1000GENOMES	ss238115000	Jul 15, 2010 (132)
26	BL	ss252864170	May 09, 2011 (134)
27	GMI	ss275680896	May 04, 2012 (137)
28	GMI	ss283987405	Apr 25, 2013 (138)
29	PJP	ss290493812	May 09, 2011 (134)
30	ILLUMINA	ss481631661	Sep 08, 2015 (146)
31	ILLUMINA	ss537154856	Sep 08, 2015 (146)
32	SSMP	ss647516315	Apr 25, 2013 (138)
33	EVA-GONL	ss974769508	Aug 21, 2014 (142)
34	JMKIDD_LAB	ss1067612393	Aug 21, 2014 (142)
35	1000GENOMES	ss1289339838	Aug 21, 2014 (142)
36	DDI	ss1425684898	Apr 01, 2015 (144)
37	EVA_GENOME_DK	ss1573851186	Apr 01, 2015 (144)
38	EVA_DECODE	ss1584129568	Apr 01, 2015 (144)
39	EVA_UK10K_ALSPAC	ss1599378495	Apr 01, 2015 (144)
40	EVA_UK10K_TWINSUK	ss1642372528	Apr 01, 2015 (144)
41	EVA_SVP	ss1712305465	Apr 01, 2015 (144)
42	WEILL_CORNELL_DGM	ss1917960572	Feb 12, 2016 (147)
43	GENOMED	ss1966667343	Jul 19, 2016 (147)
44	JJLAB	ss2019498450	Sep 14, 2016 (149)
45	USC_VALOUEV	ss2147484439	Dec 20, 2016 (150)
46	SYSTEMSBIOZJU	ss2624264797	Nov 08, 2017 (151)
47	GRF	ss2697374741	Nov 08, 2017 (151)
48	GNOMAD	ss2750640217	Nov 08, 2017 (151)
49	SWEGEN	ss2986149256	Nov 08, 2017 (151)
50	BIOINF_KMB_FNS_UNIBA	ss3023513716	Nov 08, 2017 (151)
51	CSHL	ss3343272629	Nov 08, 2017 (151)
52	ILLUMINA	ss3626006522	Oct 11, 2018 (152)
53	ILLUMINA	ss3635978608	Oct 11, 2018 (152)
54	ILLUMINA	ss3637732368	Oct 11, 2018 (152)
55	ILLUMINA	ss3642746671	Oct 11, 2018 (152)
56	URBANLAB	ss3646581237	Oct 11, 2018 (152)
57	EVA_DECODE	ss3685992319	Jul 12, 2019 (153)
58	ACPOP	ss3726716446	Jul 12, 2019 (153)
59	EVA	ss3745721098	Jul 12, 2019 (153)
60	PACBIO	ss3783302168	Jul 12, 2019 (153)
61	PACBIO	ss3788980032	Jul 12, 2019 (153)
62	PACBIO	ss3793852568	Jul 12, 2019 (153)
63	KHV_HUMAN_GENOMES	ss3798743745	Jul 12, 2019 (153)
64	EVA	ss3825981486	Apr 25, 2020 (154)
65	EVA	ss3836378439	Apr 25, 2020 (154)
66	EVA	ss3841782439	Apr 25, 2020 (154)
67	SGDP_PRJ	ss3847995800	Apr 25, 2020 (154)
68	KRGDB	ss3892836074	Apr 25, 2020 (154)
69	EVA	ss4016889041	Apr 25, 2021 (155)
70	TOPMED	ss4436436945	Apr 25, 2021 (155)
71	TOMMO_GENOMICS	ss5142052697	Apr 25, 2021 (155)
72	1000G_HIGH_COVERAGE	ss5240863865	Oct 12, 2022 (156)
73	EVA	ss5316184020	Oct 12, 2022 (156)
74	HUGCELL_USP	ss5442112462	Oct 12, 2022 (156)
75	1000G_HIGH_COVERAGE	ss5512488701	Oct 12, 2022 (156)
76	SANFORD_IMAGENETICS	ss5624749595	Oct 12, 2022 (156)
77	TOMMO_GENOMICS	ss5666192142	Oct 12, 2022 (156)
78	YY_MCH	ss5800243851	Oct 12, 2022 (156)
79	EVA	ss5831418529	Oct 12, 2022 (156)
80	EVA	ss5848748891	Oct 12, 2022 (156)
81	EVA	ss5906705040	Oct 12, 2022 (156)
82	EVA	ss5936582861	Oct 12, 2022 (156)
83	1000Genomes	NC_000001.10 - 785989	Oct 11, 2018 (152)
84	1000Genomes_30x	NC_000001.11 - 850609	Oct 12, 2022 (156)
85	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 785989	Oct 11, 2018 (152)
86	The Danish reference pan genome	NC_000001.10 - 785989	Apr 25, 2020 (154)
87	gnomAD - Genomes	NC_000001.11 - 850609	Apr 25, 2021 (155)
88	Genome of the Netherlands Release 5	NC_000001.10 - 785989	Apr 25, 2020 (154)
89	HapMap	NC_000001.11 - 850609	Apr 25, 2020 (154)
90	KOREAN population from KRGDB	NC_000001.10 - 785989	Apr 25, 2020 (154)
91	Northern Sweden	NC_000001.10 - 785989	Jul 12, 2019 (153)
92	Qatari	NC_000001.10 - 785989	Apr 25, 2020 (154)
93	SGDP_PRJ	NC_000001.10 - 785989	Apr 25, 2020 (154)
94	Siberian	NC_000001.10 - 785989	Apr 25, 2020 (154)
95	8.3KJPN	NC_000001.10 - 785989	Apr 25, 2021 (155)
96	14KJPN	NC_000001.11 - 850609	Oct 12, 2022 (156)
97	TopMed	NC_000001.11 - 850609	Apr 25, 2021 (155)
98	UK 10K study - Twins	NC_000001.10 - 785989	Oct 11, 2018 (152)
99	ALFA	NC_000001.11 - 850609	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)
rs57693175	Feb 27, 2009 (130)
rs74314548	Dec 02, 2009 (131)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
13468, ss3892836074	NC_000001.10:785988:T:A	NC_000001.11:850608:T:A	(self)
2434621584	NC_000001.11:850608:T:A	NC_000001.11:850608:T:A	(self)
ss87155983, ss107938285, ss109937332, ss118438368, ss162980873, ss197885475, ss205120721, ss252864170, ss275680896, ss283987405, ss290493812, ss1584129568, ss1712305465, ss3642746671	NC_000001.9:775851:T:C	NC_000001.11:850608:T:C	(self)
4585, 432, 1358420, 544, 13468, 1311, 2502, 12780, 793, 22004, 432, ss218190445, ss230395484, ss238115000, ss481631661, ss537154856, ss647516315, ss974769508, ss1067612393, ss1289339838, ss1425684898, ss1573851186, ss1599378495, ss1642372528, ss1917960572, ss1966667343, ss2019498450, ss2147484439, ss2624264797, ss2697374741, ss2750640217, ss2986149256, ss3343272629, ss3626006522, ss3635978608, ss3637732368, ss3726716446, ss3745721098, ss3783302168, ss3788980032, ss3793852568, ss3825981486, ss3836378439, ss3847995800, ss3892836074, ss4016889041, ss5142052697, ss5316184020, ss5624749595, ss5831418529, ss5936582861	NC_000001.10:785988:T:C	NC_000001.11:850608:T:C	(self)
14636, 68426, 78, 29246, 43280, 2434621584, ss3023513716, ss3646581237, ss3685992319, ss3798743745, ss3841782439, ss4436436945, ss5240863865, ss5442112462, ss5512488701, ss5666192142, ss5800243851, ss5848748891, ss5906705040	NC_000001.11:850608:T:C	NC_000001.11:850608:T:C	(self)
ss4194509, ss41187782, ss66317030, ss75264617, ss76002276, ss81922362, ss97913239, ss105111712, ss137752300, ss138891772, ss154522410, ss160604319, ss170255113, ss173546293	NT_004350.19:264620:T:C	NC_000001.11:850608:T:C	(self)
ss20575722	NT_034471.3:264620:T:C	NC_000001.11:850608:T:C	(self)
13468, ss3892836074	NC_000001.10:785988:T:G	NC_000001.11:850608:T:G	(self)

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

1 citation for rs2980300

PMID	Title	Author	Year	Journal
20648244	Periventricular heterotopia in common microdeletion syndromes.	van Kogelenberg M et al.	2010	Molecular syndromology

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

rs2980300