Name: rs78103748
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.

rs78103748

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:232364508 (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: C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.082553 (21851/264690, TOPMED)
T=0.070556 (9876/139974, GnomAD)
T=0.04686 (1375/29342, ALFA) (+ 17 more)
T=0.13180 (3724/28256, 14KJPN)
T=0.13180 (2209/16760, 8.3KJPN)
T=0.1046 (670/6404, 1000G_30x)
T=0.1052 (527/5008, 1000G)
T=0.0571 (256/4480, Estonian)
T=0.0752 (290/3854, ALSPAC)
T=0.0715 (265/3708, TWINSUK)
T=0.1792 (525/2930, KOREAN)
T=0.1769 (324/1832, Korea1K)
T=0.050 (50/998, GoNL)
T=0.097 (58/600, NorthernSweden)
T=0.060 (13/216, Qatari)
T=0.182 (39/214, Vietnamese)
C=0.379 (47/124, SGDP_PRJ)
T=0.05 (2/40, GENOME_DK)
C=0.50 (6/12, Siberian)
T=0.50 (6/12, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC105373196 : 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	29342	C=0.95314	T=0.04686
European	Sub	23720	C=0.94920	T=0.05080
African	Sub	3086	C=0.9961	T=0.0039
African Others	Sub	124	C=1.000	T=0.000
African American	Sub	2962	C=0.9959	T=0.0041
Asian	Sub	104	C=0.952	T=0.048
East Asian	Sub	82	C=0.95	T=0.05
Other Asian	Sub	22	C=0.95	T=0.05
Latin American 1	Sub	142	C=0.965	T=0.035
Latin American 2	Sub	426	C=0.953	T=0.047
South Asian	Sub	104	C=0.990	T=0.010
Other	Sub	1760	C=0.9278	T=0.0722

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	C=0.917447	T=0.082553
gnomAD - Genomes	Global	Study-wide	139974	C=0.929444	T=0.070556
gnomAD - Genomes	European	Sub	75824	C=0.92419	T=0.07581
gnomAD - Genomes	African	Sub	41938	C=0.98281	T=0.01719
gnomAD - Genomes	American	Sub	13618	C=0.82171	T=0.17829
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.9214	T=0.0786
gnomAD - Genomes	East Asian	Sub	3124	C=0.8329	T=0.1671
gnomAD - Genomes	Other	Sub	2150	C=0.9088	T=0.0912
Allele Frequency Aggregator	Total	Global	29342	C=0.95314	T=0.04686
Allele Frequency Aggregator	European	Sub	23720	C=0.94920	T=0.05080
Allele Frequency Aggregator	African	Sub	3086	C=0.9961	T=0.0039
Allele Frequency Aggregator	Other	Sub	1760	C=0.9278	T=0.0722
Allele Frequency Aggregator	Latin American 2	Sub	426	C=0.953	T=0.047
Allele Frequency Aggregator	Latin American 1	Sub	142	C=0.965	T=0.035
Allele Frequency Aggregator	South Asian	Sub	104	C=0.990	T=0.010
Allele Frequency Aggregator	Asian	Sub	104	C=0.952	T=0.048
14KJPN	JAPANESE	Study-wide	28256	C=0.86820	T=0.13180
8.3KJPN	JAPANESE	Study-wide	16760	C=0.86820	T=0.13180
1000Genomes_30x	Global	Study-wide	6404	C=0.8954	T=0.1046
1000Genomes_30x	African	Sub	1786	C=0.9955	T=0.0045
1000Genomes_30x	Europe	Sub	1266	C=0.9297	T=0.0703
1000Genomes_30x	South Asian	Sub	1202	C=0.9243	T=0.0757
1000Genomes_30x	East Asian	Sub	1170	C=0.8197	T=0.1803
1000Genomes_30x	American	Sub	980	C=0.723	T=0.277
1000Genomes	Global	Study-wide	5008	C=0.8948	T=0.1052
1000Genomes	African	Sub	1322	C=0.9947	T=0.0053
1000Genomes	East Asian	Sub	1008	C=0.8194	T=0.1806
1000Genomes	Europe	Sub	1006	C=0.9254	T=0.0746
1000Genomes	South Asian	Sub	978	C=0.922	T=0.078
1000Genomes	American	Sub	694	C=0.731	T=0.269
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9429	T=0.0571
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9248	T=0.0752
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9285	T=0.0715
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.8208	T=0.1792
Korean Genome Project	KOREAN	Study-wide	1832	C=0.8231	T=0.1769
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.950	T=0.050
Northern Sweden	ACPOP	Study-wide	600	C=0.903	T=0.097
Qatari	Global	Study-wide	216	C=0.940	T=0.060
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.818	T=0.182
SGDP_PRJ	Global	Study-wide	124	C=0.379	T=0.621
The Danish reference pan genome	Danish	Study-wide	40	C=0.95	T=0.05
Siberian	Global	Study-wide	12	C=0.50	T=0.50

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.232364508C>T
GRCh37.p13 chr 1	NC_000001.10:g.232500254C>T

Gene: LOC105373196, uncharacterized LOC105373196 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105373196 transcript variant X1	XR_949273.2: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	C=	T
GRCh38.p14 chr 1	NC_000001.11:g.232364508=	NC_000001.11:g.232364508C>T
GRCh37.p13 chr 1	NC_000001.10:g.232500254=	NC_000001.10:g.232500254C>T

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#.

56 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss230945833	Jul 14, 2010 (132)
2	1000GENOMES	ss238551639	Jul 15, 2010 (132)
3	GMI	ss276261006	May 04, 2012 (137)
4	ILLUMINA	ss482260762	May 04, 2012 (137)
5	ILLUMINA	ss482943426	May 04, 2012 (137)
6	ILLUMINA	ss534854695	Sep 08, 2015 (146)
7	SSMP	ss648781367	Apr 25, 2013 (138)
8	ILLUMINA	ss780103016	Sep 08, 2015 (146)
9	ILLUMINA	ss781929290	Sep 08, 2015 (146)
10	ILLUMINA	ss835585610	Sep 08, 2015 (146)
11	EVA-GONL	ss976259233	Aug 21, 2014 (142)
12	JMKIDD_LAB	ss1068688135	Aug 21, 2014 (142)
13	1000GENOMES	ss1295082325	Aug 21, 2014 (142)
14	DDI	ss1426144488	Apr 01, 2015 (144)
15	EVA_GENOME_DK	ss1574751507	Apr 01, 2015 (144)
16	EVA_DECODE	ss1585659076	Apr 01, 2015 (144)
17	EVA_UK10K_ALSPAC	ss1602370042	Apr 01, 2015 (144)
18	EVA_UK10K_TWINSUK	ss1645364075	Apr 01, 2015 (144)
19	WEILL_CORNELL_DGM	ss1919480547	Feb 12, 2016 (147)
20	GENOMED	ss1966999789	Jul 19, 2016 (147)
21	JJLAB	ss2020265567	Sep 14, 2016 (149)
22	USC_VALOUEV	ss2148301563	Dec 20, 2016 (150)
23	HUMAN_LONGEVITY	ss2170977092	Dec 20, 2016 (150)
24	SYSTEMSBIOZJU	ss2624645143	Nov 08, 2017 (151)
25	ILLUMINA	ss2632643457	Nov 08, 2017 (151)
26	ILLUMINA	ss2632643458	Nov 08, 2017 (151)
27	GRF	ss2698302443	Nov 08, 2017 (151)
28	GNOMAD	ss2767441580	Nov 08, 2017 (151)
29	SWEGEN	ss2988628526	Nov 08, 2017 (151)
30	BIOINF_KMB_FNS_UNIBA	ss3023893670	Nov 08, 2017 (151)
31	CSHL	ss3343962490	Nov 08, 2017 (151)
32	ILLUMINA	ss3626333797	Oct 11, 2018 (152)
33	ILLUMINA	ss3630672576	Oct 11, 2018 (152)
34	ILLUMINA	ss3641646265	Oct 11, 2018 (152)
35	EGCUT_WGS	ss3656587341	Jul 12, 2019 (153)
36	EVA_DECODE	ss3688842441	Jul 12, 2019 (153)
37	ACPOP	ss3727956492	Jul 12, 2019 (153)
38	EVA	ss3747472536	Jul 12, 2019 (153)
39	KHV_HUMAN_GENOMES	ss3800474392	Jul 12, 2019 (153)
40	SGDP_PRJ	ss3851123175	Apr 25, 2020 (154)
41	KRGDB	ss3896472021	Apr 25, 2020 (154)
42	KOGIC	ss3946717727	Apr 25, 2020 (154)
43	TOPMED	ss4487359608	Apr 25, 2021 (155)
44	TOMMO_GENOMICS	ss5148928411	Apr 25, 2021 (155)
45	1000G_HIGH_COVERAGE	ss5246173160	Oct 12, 2022 (156)
46	EVA	ss5314691052	Oct 12, 2022 (156)
47	EVA	ss5325480202	Oct 12, 2022 (156)
48	HUGCELL_USP	ss5446571194	Oct 12, 2022 (156)
49	1000G_HIGH_COVERAGE	ss5520459901	Oct 12, 2022 (156)
50	SANFORD_IMAGENETICS	ss5627661449	Oct 12, 2022 (156)
51	TOMMO_GENOMICS	ss5676832721	Oct 12, 2022 (156)
52	YY_MCH	ss5801735752	Oct 12, 2022 (156)
53	EVA	ss5833415209	Oct 12, 2022 (156)
54	EVA	ss5849333743	Oct 12, 2022 (156)
55	EVA	ss5912408518	Oct 12, 2022 (156)
56	EVA	ss5939509891	Oct 12, 2022 (156)
57	1000Genomes	NC_000001.10 - 232500254	Oct 11, 2018 (152)
58	1000Genomes_30x	NC_000001.11 - 232364508	Oct 12, 2022 (156)
59	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 232500254	Oct 11, 2018 (152)
60	Genetic variation in the Estonian population	NC_000001.10 - 232500254	Oct 11, 2018 (152)
61	The Danish reference pan genome	NC_000001.10 - 232500254	Apr 25, 2020 (154)
62	gnomAD - Genomes	NC_000001.11 - 232364508	Apr 25, 2021 (155)
63	Genome of the Netherlands Release 5	NC_000001.10 - 232500254	Apr 25, 2020 (154)
64	KOREAN population from KRGDB	NC_000001.10 - 232500254	Apr 25, 2020 (154)
65	Korean Genome Project	NC_000001.11 - 232364508	Apr 25, 2020 (154)
66	Northern Sweden	NC_000001.10 - 232500254	Jul 12, 2019 (153)
67	Qatari	NC_000001.10 - 232500254	Apr 25, 2020 (154)
68	SGDP_PRJ	NC_000001.10 - 232500254	Apr 25, 2020 (154)
69	Siberian	NC_000001.10 - 232500254	Apr 25, 2020 (154)
70	8.3KJPN	NC_000001.10 - 232500254	Apr 25, 2021 (155)
71	14KJPN	NC_000001.11 - 232364508	Oct 12, 2022 (156)
72	TopMed	NC_000001.11 - 232364508	Apr 25, 2021 (155)
73	UK 10K study - Twins	NC_000001.10 - 232500254	Oct 11, 2018 (152)
74	A Vietnamese Genetic Variation Database	NC_000001.10 - 232500254	Jul 12, 2019 (153)
75	ALFA	NC_000001.11 - 232364508	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss276261006, ss482260762, ss1585659076	NC_000001.9:230566876:C:T	NC_000001.11:232364507:C:T	(self)
5952508, 3291872, 2325589, 1930389, 1439251, 3649415, 1241357, 1522477, 3140155, 817917, 6897718, 3291872, 716152, ss230945833, ss238551639, ss482943426, ss534854695, ss648781367, ss780103016, ss781929290, ss835585610, ss976259233, ss1068688135, ss1295082325, ss1426144488, ss1574751507, ss1602370042, ss1645364075, ss1919480547, ss1966999789, ss2020265567, ss2148301563, ss2624645143, ss2632643457, ss2632643458, ss2698302443, ss2767441580, ss2988628526, ss3343962490, ss3626333797, ss3630672576, ss3641646265, ss3656587341, ss3727956492, ss3747472536, ss3851123175, ss3896472021, ss5148928411, ss5314691052, ss5325480202, ss5627661449, ss5833415209, ss5939509891	NC_000001.10:232500253:C:T	NC_000001.11:232364507:C:T	(self)
7985836, 42691964, 3095728, 10669825, 50965943, 12822720597, ss2170977092, ss3023893670, ss3688842441, ss3800474392, ss3946717727, ss4487359608, ss5246173160, ss5446571194, ss5520459901, ss5676832721, ss5801735752, ss5849333743, ss5912408518	NC_000001.11:232364507:C:T	NC_000001.11:232364507:C:T	(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 rs78103748

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

rs78103748