Name: rs10753378
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.

rs10753378

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:3976135 (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=0.199267 (52744/264690, TOPMED)
T=0.219133 (30719/140184, GnomAD)
T=0.27202 (25895/95196, ALFA) (+ 16 more)
T=0.00032 (9/28258, 14KJPN)
T=0.00036 (6/16760, 8.3KJPN)
T=0.1432 (917/6404, 1000G_30x)
T=0.1456 (729/5008, 1000G)
T=0.3234 (1449/4480, Estonian)
T=0.2867 (1105/3854, ALSPAC)
T=0.3058 (1134/3708, TWINSUK)
T=0.0020 (6/2930, KOREAN)
T=0.263 (262/998, GoNL)
T=0.162 (137/848, HapMap)
T=0.270 (162/600, NorthernSweden)
T=0.100 (53/532, SGDP_PRJ)
T=0.227 (49/216, Qatari)
T=0.005 (1/212, Vietnamese)
T=0.23 (13/56, Siberian)
T=0.33 (13/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
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	95196	T=0.27202	C=0.72798
European	Sub	86134	T=0.28533	C=0.71467
African	Sub	3448	T=0.0945	C=0.9055
African Others	Sub	142	T=0.049	C=0.951
African American	Sub	3306	T=0.0965	C=0.9035
Asian	Sub	286	T=0.000	C=1.000
East Asian	Sub	196	T=0.000	C=1.000
Other Asian	Sub	90	T=0.00	C=1.00
Latin American 1	Sub	292	T=0.192	C=0.808
Latin American 2	Sub	1958	T=0.1420	C=0.8580
South Asian	Sub	120	T=0.308	C=0.692
Other	Sub	2958	T=0.2099	C=0.7901

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=0.199267	C=0.800733
gnomAD - Genomes	Global	Study-wide	140184	T=0.219133	C=0.780867
gnomAD - Genomes	European	Sub	75884	T=0.29867	C=0.70133
gnomAD - Genomes	African	Sub	42040	T=0.10105	C=0.89895
gnomAD - Genomes	American	Sub	13650	T=0.17619	C=0.82381
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.2810	C=0.7190
gnomAD - Genomes	East Asian	Sub	3132	T=0.0016	C=0.9984
gnomAD - Genomes	Other	Sub	2154	T=0.2149	C=0.7851
Allele Frequency Aggregator	Total	Global	95196	T=0.27202	C=0.72798
Allele Frequency Aggregator	European	Sub	86134	T=0.28533	C=0.71467
Allele Frequency Aggregator	African	Sub	3448	T=0.0945	C=0.9055
Allele Frequency Aggregator	Other	Sub	2958	T=0.2099	C=0.7901
Allele Frequency Aggregator	Latin American 2	Sub	1958	T=0.1420	C=0.8580
Allele Frequency Aggregator	Latin American 1	Sub	292	T=0.192	C=0.808
Allele Frequency Aggregator	Asian	Sub	286	T=0.000	C=1.000
Allele Frequency Aggregator	South Asian	Sub	120	T=0.308	C=0.692
14KJPN	JAPANESE	Study-wide	28258	T=0.00032	C=0.99968
8.3KJPN	JAPANESE	Study-wide	16760	T=0.00036	C=0.99964
1000Genomes_30x	Global	Study-wide	6404	T=0.1432	C=0.8568
1000Genomes_30x	African	Sub	1786	T=0.0739	C=0.9261
1000Genomes_30x	Europe	Sub	1266	T=0.2852	C=0.7148
1000Genomes_30x	South Asian	Sub	1202	T=0.2346	C=0.7654
1000Genomes_30x	East Asian	Sub	1170	T=0.0034	C=0.9966
1000Genomes_30x	American	Sub	980	T=0.141	C=0.859
1000Genomes	Global	Study-wide	5008	T=0.1456	C=0.8544
1000Genomes	African	Sub	1322	T=0.0756	C=0.9244
1000Genomes	East Asian	Sub	1008	T=0.0050	C=0.9950
1000Genomes	Europe	Sub	1006	T=0.2932	C=0.7068
1000Genomes	South Asian	Sub	978	T=0.240	C=0.760
1000Genomes	American	Sub	694	T=0.135	C=0.865
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.3234	C=0.6766
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.2867	C=0.7133
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.3058	C=0.6942
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.0020	A=0.0000, C=0.9980, G=0.0000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.263	C=0.737
HapMap	Global	Study-wide	848	T=0.162	C=0.838
HapMap	American	Sub	388	T=0.206	C=0.794
HapMap	Asian	Sub	170	T=0.006	C=0.994
HapMap	Europe	Sub	170	T=0.300	C=0.700
HapMap	African	Sub	120	T=0.042	C=0.958
Northern Sweden	ACPOP	Study-wide	600	T=0.270	C=0.730
SGDP_PRJ	Global	Study-wide	532	T=0.100	C=0.900
Qatari	Global	Study-wide	216	T=0.227	C=0.773
A Vietnamese Genetic Variation Database	Global	Study-wide	212	T=0.005	C=0.995
Siberian	Global	Study-wide	56	T=0.23	C=0.77
The Danish reference pan genome	Danish	Study-wide	40	T=0.33	C=0.68

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.3976135T>A
GRCh38.p14 chr 1	NC_000001.11:g.3976135T>C
GRCh38.p14 chr 1	NC_000001.11:g.3976135T>G
GRCh37.p13 chr 1	NC_000001.10:g.4036195T>A
GRCh37.p13 chr 1	NC_000001.10:g.4036195T>C
GRCh37.p13 chr 1	NC_000001.10:g.4036195T>G

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.3976135=	NC_000001.11:g.3976135T>A	NC_000001.11:g.3976135T>C	NC_000001.11:g.3976135T>G
GRCh37.p13 chr 1	NC_000001.10:g.4036195=	NC_000001.10:g.4036195T>A	NC_000001.10:g.4036195T>C	NC_000001.10:g.4036195T>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#.

100 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss15413671	Feb 27, 2004 (120)
2	CSHL-HAPMAP	ss17344117	Feb 27, 2004 (120)
3	SC_SNP	ss18089432	Feb 27, 2004 (120)
4	SC_SNP	ss18164471	Feb 27, 2004 (120)
5	SSAHASNP	ss20513875	Apr 05, 2004 (121)
6	HGSV	ss78671099	Dec 07, 2007 (129)
7	KRIBB_YJKIM	ss82755009	Dec 16, 2007 (130)
8	HGSV	ss86042377	Dec 14, 2007 (130)
9	HUMANGENOME_JCVI	ss97915703	Feb 04, 2009 (130)
10	1000GENOMES	ss107950199	Jan 22, 2009 (130)
11	ILLUMINA-UK	ss118454671	Dec 01, 2009 (131)
12	ENSEMBL	ss138967083	Dec 01, 2009 (131)
13	GMI	ss154562140	Dec 01, 2009 (131)
14	COMPLETE_GENOMICS	ss163007430	Jul 04, 2010 (132)
15	COMPLETE_GENOMICS	ss163741663	Jul 04, 2010 (132)
16	COMPLETE_GENOMICS	ss166011854	Jul 04, 2010 (132)
17	BUSHMAN	ss197928223	Jul 04, 2010 (132)
18	BCM-HGSC-SUB	ss205071239	Jul 04, 2010 (132)
19	1000GENOMES	ss210455258	Jul 14, 2010 (132)
20	1000GENOMES	ss218204373	Jul 14, 2010 (132)
21	1000GENOMES	ss230404905	Jul 14, 2010 (132)
22	1000GENOMES	ss238123705	Jul 15, 2010 (132)
23	GMI	ss275692161	May 04, 2012 (137)
24	GMI	ss283991319	Apr 25, 2013 (138)
25	PJP	ss290498725	May 09, 2011 (134)
26	ILLUMINA	ss479332418	May 04, 2012 (142)
27	ILLUMINA	ss479335481	May 04, 2012 (142)
28	ILLUMINA	ss484466414	May 04, 2012 (142)
29	ILLUMINA	ss536628881	Sep 08, 2015 (146)
30	TISHKOFF	ss553736083	Apr 25, 2013 (138)
31	SSMP	ss647537684	Apr 25, 2013 (138)
32	ILLUMINA	ss778362987	Aug 21, 2014 (142)
33	ILLUMINA	ss782679773	Aug 21, 2014 (142)
34	ILLUMINA	ss783648292	Aug 21, 2014 (142)
35	ILLUMINA	ss831930544	Apr 01, 2015 (144)
36	ILLUMINA	ss833817784	Aug 21, 2014 (142)
37	EVA-GONL	ss974798147	Aug 21, 2014 (142)
38	JMKIDD_LAB	ss1067628669	Aug 21, 2014 (142)
39	1000GENOMES	ss1289457610	Aug 21, 2014 (142)
40	DDI	ss1425693672	Apr 01, 2015 (144)
41	EVA_GENOME_DK	ss1573860918	Apr 01, 2015 (144)
42	EVA_DECODE	ss1584156870	Apr 01, 2015 (144)
43	EVA_UK10K_ALSPAC	ss1599430445	Apr 01, 2015 (144)
44	EVA_UK10K_TWINSUK	ss1642424478	Apr 01, 2015 (144)
45	EVA_SVP	ss1712306893	Apr 01, 2015 (144)
46	ILLUMINA	ss1751919225	Sep 08, 2015 (146)
47	HAMMER_LAB	ss1793788443	Sep 08, 2015 (146)
48	WEILL_CORNELL_DGM	ss1917993750	Feb 12, 2016 (147)
49	GENOMED	ss1966671828	Jul 19, 2016 (147)
50	JJLAB	ss2019513189	Sep 14, 2016 (149)
51	USC_VALOUEV	ss2147503587	Dec 20, 2016 (150)
52	HUMAN_LONGEVITY	ss2159586454	Dec 20, 2016 (150)
53	SYSTEMSBIOZJU	ss2624272334	Nov 08, 2017 (151)
54	ILLUMINA	ss2632468964	Nov 08, 2017 (151)
55	GRF	ss2697397755	Nov 08, 2017 (151)
56	GNOMAD	ss2750987307	Nov 08, 2017 (151)
57	SWEGEN	ss2986203832	Nov 08, 2017 (151)
58	BIOINF_KMB_FNS_UNIBA	ss3023520289	Nov 08, 2017 (151)
59	CSHL	ss3343289857	Nov 08, 2017 (151)
60	ILLUMINA	ss3626012410	Oct 11, 2018 (152)
61	ILLUMINA	ss3630508244	Oct 11, 2018 (152)
62	ILLUMINA	ss3633572260	Oct 11, 2018 (152)
63	ILLUMINA	ss3634303618	Oct 11, 2018 (152)
64	ILLUMINA	ss3635266437	Oct 11, 2018 (152)
65	ILLUMINA	ss3637016789	Oct 11, 2018 (152)
66	ILLUMINA	ss3637733860	Oct 11, 2018 (152)
67	ILLUMINA	ss3640010983	Oct 11, 2018 (152)
68	ILLUMINA	ss3642748070	Oct 11, 2018 (152)
69	URBANLAB	ss3646587203	Oct 11, 2018 (152)
70	EGCUT_WGS	ss3654304977	Jul 12, 2019 (153)
71	EVA_DECODE	ss3686050588	Jul 12, 2019 (153)
72	ACPOP	ss3726741584	Jul 12, 2019 (153)
73	ILLUMINA	ss3744604613	Jul 12, 2019 (153)
74	EVA	ss3745757429	Jul 12, 2019 (153)
75	ILLUMINA	ss3772106268	Jul 12, 2019 (153)
76	PACBIO	ss3783309290	Jul 12, 2019 (153)
77	PACBIO	ss3788986156	Jul 12, 2019 (153)
78	PACBIO	ss3793858783	Jul 12, 2019 (153)
79	KHV_HUMAN_GENOMES	ss3798779148	Jul 12, 2019 (153)
80	EVA	ss3825994934	Apr 25, 2020 (154)
81	EVA	ss3836384673	Apr 25, 2020 (154)
82	EVA	ss3841788878	Apr 25, 2020 (154)
83	SGDP_PRJ	ss3848073005	Apr 25, 2020 (154)
84	KRGDB	ss3892934743	Apr 25, 2020 (154)
85	EVA	ss4016890191	Apr 25, 2021 (155)
86	TOPMED	ss4437349342	Apr 25, 2021 (155)
87	TOMMO_GENOMICS	ss5142208265	Apr 25, 2021 (155)
88	1000G_HIGH_COVERAGE	ss5240973827	Oct 12, 2022 (156)
89	EVA	ss5314587947	Oct 12, 2022 (156)
90	EVA	ss5316382890	Oct 12, 2022 (156)
91	HUGCELL_USP	ss5442198806	Oct 12, 2022 (156)
92	EVA	ss5505751985	Oct 12, 2022 (156)
93	1000G_HIGH_COVERAGE	ss5512641628	Oct 12, 2022 (156)
94	SANFORD_IMAGENETICS	ss5624811841	Oct 12, 2022 (156)
95	TOMMO_GENOMICS	ss5666424484	Oct 12, 2022 (156)
96	YY_MCH	ss5800273201	Oct 12, 2022 (156)
97	EVA	ss5831461926	Oct 12, 2022 (156)
98	EVA	ss5848760034	Oct 12, 2022 (156)
99	EVA	ss5906817214	Oct 12, 2022 (156)
100	EVA	ss5936636621	Oct 12, 2022 (156)
101	1000Genomes	NC_000001.10 - 4036195	Oct 11, 2018 (152)
102	1000Genomes_30x	NC_000001.11 - 3976135	Oct 12, 2022 (156)
103	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 4036195	Oct 11, 2018 (152)
104	Genetic variation in the Estonian population	NC_000001.10 - 4036195	Oct 11, 2018 (152)
105	The Danish reference pan genome	NC_000001.10 - 4036195	Apr 25, 2020 (154)
106	gnomAD - Genomes	NC_000001.11 - 3976135	Apr 25, 2021 (155)
107	Genome of the Netherlands Release 5	NC_000001.10 - 4036195	Apr 25, 2020 (154)
108	HapMap	NC_000001.11 - 3976135	Apr 25, 2020 (154)
109	KOREAN population from KRGDB	NC_000001.10 - 4036195	Apr 25, 2020 (154)
110	Northern Sweden	NC_000001.10 - 4036195	Jul 12, 2019 (153)
111	Qatari	NC_000001.10 - 4036195	Apr 25, 2020 (154)
112	SGDP_PRJ	NC_000001.10 - 4036195	Apr 25, 2020 (154)
113	Siberian	NC_000001.10 - 4036195	Apr 25, 2020 (154)
114	8.3KJPN	NC_000001.10 - 4036195	Apr 25, 2021 (155)
115	14KJPN	NC_000001.11 - 3976135	Oct 12, 2022 (156)
116	TopMed	NC_000001.11 - 3976135	Apr 25, 2021 (155)
117	UK 10K study - Twins	NC_000001.10 - 4036195	Oct 11, 2018 (152)
118	A Vietnamese Genetic Variation Database	NC_000001.10 - 4036195	Jul 12, 2019 (153)
119	ALFA	NC_000001.11 - 3976135	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)
rs56489210	May 24, 2008 (130)
rs57657955	May 24, 2008 (130)
rs61338391	Feb 26, 2009 (130)
rs111195643	Aug 21, 2014 (142)
rs201510385	Aug 21, 2014 (142)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
112137, ss3892934743	NC_000001.10:4036194:T:A	NC_000001.11:3976134:T:A	(self)
ss78671099, ss86042377	NC_000001.8:3946567:T:C	NC_000001.11:3976134:T:C	(self)
ss107950199, ss118454671, ss163007430, ss163741663, ss166011854, ss197928223, ss205071239, ss210455258, ss275692161, ss283991319, ss290498725, ss479332418, ss1584156870, ss1712306893, ss3642748070	NC_000001.9:3936054:T:C	NC_000001.11:3976134:T:C	(self)
125858, 57013, 43225, 1368152, 24697, 112137, 26449, 35680, 89985, 19941, 177572, 57013, 12216, ss218204373, ss230404905, ss238123705, ss479335481, ss484466414, ss536628881, ss553736083, ss647537684, ss778362987, ss782679773, ss783648292, ss831930544, ss833817784, ss974798147, ss1067628669, ss1289457610, ss1425693672, ss1573860918, ss1599430445, ss1642424478, ss1751919225, ss1793788443, ss1917993750, ss1966671828, ss2019513189, ss2147503587, ss2624272334, ss2632468964, ss2697397755, ss2750987307, ss2986203832, ss3343289857, ss3626012410, ss3630508244, ss3633572260, ss3634303618, ss3635266437, ss3637016789, ss3637733860, ss3640010983, ss3654304977, ss3726741584, ss3744604613, ss3745757429, ss3772106268, ss3783309290, ss3788986156, ss3793858783, ss3825994934, ss3836384673, ss3848073005, ss3892934743, ss4016890191, ss5142208265, ss5314587947, ss5316382890, ss5505751985, ss5624811841, ss5831461926, ss5936636621	NC_000001.10:4036194:T:C	NC_000001.11:3976134:T:C	(self)
167563, 901983, 3075, 261588, 955677, 10391420043, ss2159586454, ss3023520289, ss3646587203, ss3686050588, ss3798779148, ss3841788878, ss4437349342, ss5240973827, ss5442198806, ss5512641628, ss5666424484, ss5800273201, ss5848760034, ss5906817214	NC_000001.11:3976134:T:C	NC_000001.11:3976134:T:C	(self)
ss15413671, ss17344117, ss18089432, ss18164471, ss20513875	NT_004547.16:39827:T:C	NC_000001.11:3976134:T:C	(self)
ss82755009, ss97915703, ss138967083, ss154562140	NT_021937.19:40926:T:C	NC_000001.11:3976134:T:C	(self)
112137, ss3892934743	NC_000001.10:4036194:T:G	NC_000001.11:3976134:T:G	(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 rs10753378

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs10753378