Name: rs10751453
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.

rs10751453

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:783175 (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
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.000125 (33/264690, TOPMED)
T=0.000114 (16/139886, GnomAD)
T=0.00004 (1/28258, 14KJPN) (+ 11 more)
T=0.00006 (1/17338, ALFA)
T=0.00006 (1/16760, 8.3KJPN)
T=0.0002 (1/6404, 1000G_30x)
T=0.0010 (3/2930, KOREAN)
T=0.0000 (0/1832, Korea1K)
T=0.000 (0/600, NorthernSweden)
T=0.000 (0/558, SGDP_PRJ)
T=0.028 (15/534, MGP)
T=0.000 (0/216, Qatari)
T=0.00 (0/40, GENOME_DK)
T=0.00 (0/40, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LINC01409 : Non Coding Transcript 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	17338	T=0.00006	A=0.00000, C=0.99994
European	Sub	13496	T=0.00000	A=0.00000, C=1.00000
African	Sub	2376	T=0.0004	A=0.0000, C=0.9996
African Others	Sub	90	T=0.00	A=0.00, C=1.00
African American	Sub	2286	T=0.0004	A=0.0000, C=0.9996
Asian	Sub	112	T=0.000	A=0.000, C=1.000
East Asian	Sub	86	T=0.00	A=0.00, C=1.00
Other Asian	Sub	26	T=0.00	A=0.00, C=1.00
Latin American 1	Sub	146	T=0.000	A=0.000, C=1.000
Latin American 2	Sub	610	T=0.000	A=0.000, C=1.000
South Asian	Sub	98	T=0.00	A=0.00, C=1.00
Other	Sub	500	T=0.000	A=0.000, C=1.000

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=0.000125	C=0.999875
gnomAD - Genomes	Global	Study-wide	139886	T=0.000114	C=0.999886
gnomAD - Genomes	European	Sub	75852	T=0.00001	C=0.99999
gnomAD - Genomes	African	Sub	41838	T=0.00033	C=0.99967
gnomAD - Genomes	American	Sub	13592	T=0.00000	C=1.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=0.0003	C=0.9997
gnomAD - Genomes	East Asian	Sub	3134	T=0.0000	C=1.0000
gnomAD - Genomes	Other	Sub	2150	T=0.0000	C=1.0000
14KJPN	JAPANESE	Study-wide	28258	T=0.00004	C=0.99996
Allele Frequency Aggregator	Total	Global	17338	T=0.00006	A=0.00000, C=0.99994
Allele Frequency Aggregator	European	Sub	13496	T=0.00000	A=0.00000, C=1.00000
Allele Frequency Aggregator	African	Sub	2376	T=0.0004	A=0.0000, C=0.9996
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.000	A=0.000, C=1.000
Allele Frequency Aggregator	Other	Sub	500	T=0.000	A=0.000, C=1.000
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.000	A=0.000, C=1.000
Allele Frequency Aggregator	Asian	Sub	112	T=0.000	A=0.000, C=1.000
Allele Frequency Aggregator	South Asian	Sub	98	T=0.00	A=0.00, C=1.00
8.3KJPN	JAPANESE	Study-wide	16760	T=0.00006	C=0.99994
1000Genomes_30x	Global	Study-wide	6404	T=0.0002	C=0.9998
1000Genomes_30x	African	Sub	1786	T=0.0006	C=0.9994
1000Genomes_30x	Europe	Sub	1266	T=0.0000	C=1.0000
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=0.000	C=1.000
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.0010	C=0.9990
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=0.000	C=1.000
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	T=0.028	C=0.972
Qatari	Global	Study-wide	216	T=0.000	C=1.000
The Danish reference pan genome	Danish	Study-wide	40	T=0.00	C=1.00
Siberian	Global	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.783175T>A
GRCh38.p14 chr 1	NC_000001.11:g.783175T>C
GRCh37.p13 chr 1	NC_000001.10:g.718555T>A
GRCh37.p13 chr 1	NC_000001.10:g.718555T>C

Gene: LINC01409, uncharacterized LINC01409 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC01409 transcript variant X1	XR_007065319.1:n.1574T>A	N/A	Non Coding Transcript Variant
LINC01409 transcript variant X1	XR_007065319.1:n.1574T>C	N/A	Non Coding Transcript Variant
LINC01409 transcript variant X2	XR_007065320.1:n.	N/A	Intron 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
GRCh38.p14 chr 1	NC_000001.11:g.783175=	NC_000001.11:g.783175T>A	NC_000001.11:g.783175T>C
GRCh37.p13 chr 1	NC_000001.10:g.718555=	NC_000001.10:g.718555T>A	NC_000001.10:g.718555T>C
LINC01409 transcript variant X1	XR_007065319.1:n.1574=	XR_007065319.1:n.1574T>A	XR_007065319.1:n.1574T>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#.

55 SubSNP, 14 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss15452115	Feb 28, 2004 (124)
2	CSHL-HAPMAP	ss16428298	Feb 27, 2004 (120)
3	SC_SNP	ss18099949	Feb 27, 2004 (120)
4	SC_SNP	ss18179609	Feb 27, 2004 (120)
5	SC_SNP	ss18359537	Feb 27, 2004 (120)
6	CSHL-HAPMAP	ss19128516	Feb 27, 2004 (120)
7	HGSV	ss84605348	Dec 14, 2007 (130)
8	BCMHGSC_JDW	ss87155363	Mar 23, 2008 (129)
9	HUMANGENOME_JCVI	ss97913174	Feb 04, 2009 (130)
10	ENSEMBL	ss137751610	Dec 01, 2009 (131)
11	ENSEMBL	ss138907119	Dec 01, 2009 (131)
12	GMI	ss154522237	Dec 01, 2009 (131)
13	BUSHMAN	ss197885304	Jul 04, 2010 (132)
14	BL	ss252864000	May 09, 2011 (134)
15	GMI	ss275680540	May 04, 2012 (137)
16	GMI	ss283987301	Apr 25, 2013 (138)
17	PJP	ss290493752	May 09, 2011 (134)
18	1000GENOMES	ss328357092	May 09, 2011 (134)
19	SSMP	ss647515857	Apr 25, 2013 (138)
20	JMKIDD_LAB	ss1067612312	Aug 21, 2014 (142)
21	DDI	ss1425684727	Apr 01, 2015 (144)
22	EVA_GENOME_DK	ss1573851061	Apr 01, 2015 (144)
23	EVA_MGP	ss1710883331	Apr 01, 2015 (144)
24	WEILL_CORNELL_DGM	ss1917959739	Feb 12, 2016 (147)
25	GENOMED	ss1966667309	Jul 19, 2016 (147)
26	USC_VALOUEV	ss2147483829	Dec 20, 2016 (150)
27	SYSTEMSBIOZJU	ss2624264727	Nov 08, 2017 (151)
28	GRF	ss2697374026	Nov 08, 2017 (151)
29	GNOMAD	ss2750633121	Nov 08, 2017 (151)
30	SWEGEN	ss2986147741	Nov 08, 2017 (151)
31	CSHL	ss3343272186	Nov 08, 2017 (151)
32	URBANLAB	ss3646581101	Oct 11, 2018 (152)
33	EVA_DECODE	ss3685991640	Jul 12, 2019 (153)
34	ACPOP	ss3726715989	Jul 12, 2019 (153)
35	EVA	ss3745720705	Jul 12, 2019 (153)
36	PACBIO	ss3783302028	Jul 12, 2019 (153)
37	PACBIO	ss3788979910	Jul 12, 2019 (153)
38	PACBIO	ss3793852447	Jul 12, 2019 (153)
39	KHV_HUMAN_GENOMES	ss3798743101	Jul 12, 2019 (153)
40	EVA	ss3825981371	Apr 25, 2020 (154)
41	EVA	ss3836378316	Apr 25, 2020 (154)
42	EVA	ss3841782314	Apr 25, 2020 (154)
43	SGDP_PRJ	ss3847993845	Apr 25, 2020 (154)
44	KRGDB	ss3892833284	Apr 25, 2020 (154)
45	KOGIC	ss3943628392	Apr 25, 2020 (154)
46	TOPMED	ss4436422634	Apr 25, 2021 (155)
47	TOMMO_GENOMICS	ss5142049464	Apr 25, 2021 (155)
48	1000G_HIGH_COVERAGE	ss5512485707	Oct 12, 2022 (156)
49	SANFORD_IMAGENETICS	ss5624747902	Oct 12, 2022 (156)
50	TOMMO_GENOMICS	ss5666187763	Oct 12, 2022 (156)
51	YY_MCH	ss5800243129	Oct 12, 2022 (156)
52	EVA	ss5831417624	Oct 12, 2022 (156)
53	EVA	ss5848748804	Oct 12, 2022 (156)
54	EVA	ss5936582127	Oct 12, 2022 (156)
55	EVA	ss5979925972	Oct 12, 2022 (156)
56	1000Genomes_30x	NC_000001.11 - 783175	Oct 12, 2022 (156)
57	The Danish reference pan genome	NC_000001.10 - 718555	Apr 25, 2020 (154)
58	gnomAD - Genomes	NC_000001.11 - 783175	Apr 25, 2021 (155)
59	KOREAN population from KRGDB	NC_000001.10 - 718555	Apr 25, 2020 (154)
60	Korean Genome Project	NC_000001.11 - 783175	Apr 25, 2020 (154)
61	Medical Genome Project healthy controls from Spanish population	NC_000001.10 - 718555	Apr 25, 2020 (154)
62	Northern Sweden	NC_000001.10 - 718555	Jul 12, 2019 (153)
63	Qatari	NC_000001.10 - 718555	Apr 25, 2020 (154)
64	SGDP_PRJ	NC_000001.10 - 718555	Apr 25, 2020 (154)
65	Siberian	NC_000001.10 - 718555	Apr 25, 2020 (154)
66	8.3KJPN	NC_000001.10 - 718555	Apr 25, 2021 (155)
67	14KJPN	NC_000001.11 - 783175	Oct 12, 2022 (156)
68	TopMed	NC_000001.11 - 783175	Apr 25, 2021 (155)
69	ALFA	NC_000001.11 - 783175	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)
rs11490922	Dec 02, 2004 (124)
rs58016133	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
2300717393	NC_000001.11:783174:T:A	NC_000001.11:783174:T:A	(self)
ss84605348	NC_000001.8:758417:T:C	NC_000001.11:783174:T:C	(self)
ss87155363, ss197885304, ss252864000, ss275680540, ss283987301, ss290493752	NC_000001.9:708417:T:C	NC_000001.11:783174:T:C	(self)
1358295, 10678, 83, 854, 1669, 10825, 183, 18771, ss328357092, ss647515857, ss1067612312, ss1425684727, ss1573851061, ss1710883331, ss1917959739, ss1966667309, ss2147483829, ss2624264727, ss2697374026, ss2750633121, ss2986147741, ss3343272186, ss3726715989, ss3745720705, ss3783302028, ss3788979910, ss3793852447, ss3825981371, ss3836378316, ss3847993845, ss3892833284, ss5142049464, ss5624747902, ss5831417624, ss5936582127, ss5979925972	NC_000001.10:718554:T:C	NC_000001.11:783174:T:C	(self)
11642, 53977, 6393, 24867, 28969, 2300717393, ss3646581101, ss3685991640, ss3798743101, ss3841782314, ss3943628392, ss4436422634, ss5512485707, ss5666187763, ss5800243129, ss5848748804	NC_000001.11:783174:T:C	NC_000001.11:783174:T:C	(self)
ss15452115, ss97913174, ss137751610, ss138907119, ss154522237	NT_004350.19:197186:T:C	NC_000001.11:783174:T:C	(self)
ss16428298, ss18099949, ss18179609, ss18359537, ss19128516	NT_034471.3:197186:T:C	NC_000001.11:783174: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 rs10751453

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

rs10751453