Name: rs1497378
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.

rs1497378

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:99236866 (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>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.371193 (98251/264690, TOPMED)
G=0.378474 (52894/139756, GnomAD)
G=0.09675 (2734/28258, 14KJPN) (+ 14 more)
G=0.41149 (7773/18890, ALFA)
G=0.09320 (1562/16760, 8.3KJPN)
G=0.2794 (1789/6404, 1000G_30x)
G=0.2734 (1369/5008, 1000G)
G=0.4433 (1986/4480, Estonian)
G=0.4650 (1792/3854, ALSPAC)
G=0.4803 (1781/3708, TWINSUK)
G=0.1400 (409/2922, KOREAN)
G=0.448 (447/998, GoNL)
G=0.482 (289/600, NorthernSweden)
T=0.389 (115/296, SGDP_PRJ)
G=0.361 (78/216, Qatari)
T=0.29 (12/42, Siberian)
G=0.38 (15/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC100507053 : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	18890	T=0.58851	G=0.41149	0.352356	0.175331	0.472313	4
European	Sub	14286	T=0.53878	G=0.46122	0.282234	0.204676	0.51309	5
African	Sub	2946	T=0.8306	G=0.1694	0.684997	0.023761	0.291242	1
African Others	Sub	114	T=0.877	G=0.123	0.789474	0.035088	0.175439	1
African American	Sub	2832	T=0.8287	G=0.1713	0.680791	0.023305	0.295904	2
Asian	Sub	112	T=0.929	G=0.071	0.857143	0.0	0.142857	0
East Asian	Sub	86	T=0.93	G=0.07	0.860465	0.0	0.139535	0
Other Asian	Sub	26	T=0.92	G=0.08	0.846154	0.0	0.153846	0
Latin American 1	Sub	146	T=0.521	G=0.479	0.30137	0.260274	0.438356	1
Latin American 2	Sub	610	T=0.495	G=0.505	0.242623	0.252459	0.504918	0
South Asian	Sub	98	T=0.83	G=0.17	0.714286	0.061224	0.22449	2
Other	Sub	692	T=0.592	G=0.408	0.358382	0.17341	0.468208	0

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=0.628807	G=0.371193
gnomAD - Genomes	Global	Study-wide	139756	T=0.621526	G=0.378474
gnomAD - Genomes	European	Sub	75616	T=0.53379	G=0.46621
gnomAD - Genomes	African	Sub	41976	T=0.81613	G=0.18387
gnomAD - Genomes	American	Sub	13568	T=0.49713	G=0.50287
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=0.4524	G=0.5476
gnomAD - Genomes	East Asian	Sub	3128	T=0.8721	G=0.1279
gnomAD - Genomes	Other	Sub	2148	T=0.5894	G=0.4106
14KJPN	JAPANESE	Study-wide	28258	T=0.90325	G=0.09675
Allele Frequency Aggregator	Total	Global	18890	T=0.58851	G=0.41149
Allele Frequency Aggregator	European	Sub	14286	T=0.53878	G=0.46122
Allele Frequency Aggregator	African	Sub	2946	T=0.8306	G=0.1694
Allele Frequency Aggregator	Other	Sub	692	T=0.592	G=0.408
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.495	G=0.505
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.521	G=0.479
Allele Frequency Aggregator	Asian	Sub	112	T=0.929	G=0.071
Allele Frequency Aggregator	South Asian	Sub	98	T=0.83	G=0.17
8.3KJPN	JAPANESE	Study-wide	16760	T=0.90680	G=0.09320
1000Genomes_30x	Global	Study-wide	6404	T=0.7206	G=0.2794
1000Genomes_30x	African	Sub	1786	T=0.8623	G=0.1377
1000Genomes_30x	Europe	Sub	1266	T=0.5055	G=0.4945
1000Genomes_30x	South Asian	Sub	1202	T=0.8270	G=0.1730
1000Genomes_30x	East Asian	Sub	1170	T=0.8667	G=0.1333
1000Genomes_30x	American	Sub	980	T=0.436	G=0.564
1000Genomes	Global	Study-wide	5008	T=0.7266	G=0.2734
1000Genomes	African	Sub	1322	T=0.8540	G=0.1460
1000Genomes	East Asian	Sub	1008	T=0.8750	G=0.1250
1000Genomes	Europe	Sub	1006	T=0.5080	G=0.4920
1000Genomes	South Asian	Sub	978	T=0.830	G=0.170
1000Genomes	American	Sub	694	T=0.439	G=0.561
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.5567	G=0.4433
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.5350	G=0.4650
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.5197	G=0.4803
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.8600	G=0.1400
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.552	G=0.448
Northern Sweden	ACPOP	Study-wide	600	T=0.518	G=0.482
SGDP_PRJ	Global	Study-wide	296	T=0.389	G=0.611
Qatari	Global	Study-wide	216	T=0.639	G=0.361
Siberian	Global	Study-wide	42	T=0.29	G=0.71
The Danish reference pan genome	Danish	Study-wide	40	T=0.62	G=0.38

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 4	NC_000004.12:g.99236866T>G
GRCh37.p13 chr 4	NC_000004.11:g.100158023T>G

Gene: LOC100507053, uncharacterized LOC100507053 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC100507053 transcript	NR_037884.1: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=	G
GRCh38.p14 chr 4	NC_000004.12:g.99236866=	NC_000004.12:g.99236866T>G
GRCh37.p13 chr 4	NC_000004.11:g.100158023=	NC_000004.11:g.100158023T>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#.

58 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2326279	Oct 23, 2000 (88)
2	SSAHASNP	ss22213752	Apr 05, 2004 (121)
3	ABI	ss42171909	Mar 13, 2006 (126)
4	HGSV	ss85650492	Dec 16, 2007 (130)
5	1000GENOMES	ss108170842	Jan 23, 2009 (130)
6	ILLUMINA-UK	ss117113645	Feb 14, 2009 (130)
7	ENSEMBL	ss135207923	Dec 01, 2009 (131)
8	1000GENOMES	ss221098716	Jul 14, 2010 (132)
9	1000GENOMES	ss232515070	Jul 14, 2010 (132)
10	1000GENOMES	ss239780103	Jul 15, 2010 (132)
11	GMI	ss277844356	May 04, 2012 (137)
12	PJP	ss293147482	May 09, 2011 (134)
13	SSMP	ss651525664	Apr 25, 2013 (138)
14	EVA-GONL	ss980450038	Aug 21, 2014 (142)
15	JMKIDD_LAB	ss1071787085	Aug 21, 2014 (142)
16	1000GENOMES	ss1310979706	Aug 21, 2014 (142)
17	DDI	ss1429982689	Apr 01, 2015 (144)
18	EVA_GENOME_DK	ss1580687398	Apr 01, 2015 (144)
19	EVA_DECODE	ss1589954062	Apr 01, 2015 (144)
20	EVA_UK10K_ALSPAC	ss1610736149	Apr 01, 2015 (144)
21	EVA_UK10K_TWINSUK	ss1653730182	Apr 01, 2015 (144)
22	WEILL_CORNELL_DGM	ss1923690133	Feb 12, 2016 (147)
23	GENOMED	ss1969816812	Jul 19, 2016 (147)
24	JJLAB	ss2022431008	Sep 14, 2016 (149)
25	USC_VALOUEV	ss2150560182	Dec 20, 2016 (150)
26	HUMAN_LONGEVITY	ss2265424770	Dec 20, 2016 (150)
27	GRF	ss2706037068	Nov 08, 2017 (151)
28	GNOMAD	ss2812853958	Nov 08, 2017 (151)
29	SWEGEN	ss2995210417	Nov 08, 2017 (151)
30	BIOINF_KMB_FNS_UNIBA	ss3024990769	Nov 08, 2017 (151)
31	CSHL	ss3345861779	Nov 08, 2017 (151)
32	URBANLAB	ss3647802614	Oct 12, 2018 (152)
33	EGCUT_WGS	ss3663106225	Jul 13, 2019 (153)
34	EVA_DECODE	ss3712656741	Jul 13, 2019 (153)
35	ACPOP	ss3731421746	Jul 13, 2019 (153)
36	EVA	ss3762167048	Jul 13, 2019 (153)
37	PACBIO	ss3784801941	Jul 13, 2019 (153)
38	PACBIO	ss3790246607	Jul 13, 2019 (153)
39	PACBIO	ss3795122011	Jul 13, 2019 (153)
40	KHV_HUMAN_GENOMES	ss3805315469	Jul 13, 2019 (153)
41	EVA	ss3828703511	Apr 26, 2020 (154)
42	EVA	ss3837792830	Apr 26, 2020 (154)
43	EVA	ss3843231221	Apr 26, 2020 (154)
44	SGDP_PRJ	ss3859610564	Apr 26, 2020 (154)
45	KRGDB	ss3905888020	Apr 26, 2020 (154)
46	TOPMED	ss4624638851	Apr 26, 2021 (155)
47	TOMMO_GENOMICS	ss5167078393	Apr 26, 2021 (155)
48	1000G_HIGH_COVERAGE	ss5260288444	Oct 13, 2022 (156)
49	HUGCELL_USP	ss5458930882	Oct 13, 2022 (156)
50	EVA	ss5507641450	Oct 13, 2022 (156)
51	1000G_HIGH_COVERAGE	ss5541956246	Oct 13, 2022 (156)
52	SANFORD_IMAGENETICS	ss5635665546	Oct 13, 2022 (156)
53	TOMMO_GENOMICS	ss5701809579	Oct 13, 2022 (156)
54	YY_MCH	ss5805353979	Oct 13, 2022 (156)
55	EVA	ss5844424157	Oct 13, 2022 (156)
56	EVA	ss5854355956	Oct 13, 2022 (156)
57	EVA	ss5864676969	Oct 13, 2022 (156)
58	EVA	ss5964056220	Oct 13, 2022 (156)
59	1000Genomes	NC_000004.11 - 100158023	Oct 12, 2018 (152)
60	1000Genomes_30x	NC_000004.12 - 99236866	Oct 13, 2022 (156)
61	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 100158023	Oct 12, 2018 (152)
62	Genetic variation in the Estonian population	NC_000004.11 - 100158023	Oct 12, 2018 (152)
63	The Danish reference pan genome	NC_000004.11 - 100158023	Apr 26, 2020 (154)
64	gnomAD - Genomes	NC_000004.12 - 99236866	Apr 26, 2021 (155)
65	Genome of the Netherlands Release 5	NC_000004.11 - 100158023	Apr 26, 2020 (154)
66	KOREAN population from KRGDB	NC_000004.11 - 100158023	Apr 26, 2020 (154)
67	Northern Sweden	NC_000004.11 - 100158023	Jul 13, 2019 (153)
68	Qatari	NC_000004.11 - 100158023	Apr 26, 2020 (154)
69	SGDP_PRJ	NC_000004.11 - 100158023	Apr 26, 2020 (154)
70	Siberian	NC_000004.11 - 100158023	Apr 26, 2020 (154)
71	8.3KJPN	NC_000004.11 - 100158023	Apr 26, 2021 (155)
72	14KJPN	NC_000004.12 - 99236866	Oct 13, 2022 (156)
73	TopMed	NC_000004.12 - 99236866	Apr 26, 2021 (155)
74	UK 10K study - Twins	NC_000004.11 - 100158023	Oct 12, 2018 (152)
75	ALFA	NC_000004.12 - 99236866	Apr 26, 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)
rs61057702	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss85650492	NC_000004.9:100515200:T:G	NC_000004.12:99236865:T:G	(self)
ss108170842, ss117113645, ss277844356, ss293147482, ss1589954062	NC_000004.10:100377045:T:G	NC_000004.12:99236865:T:G	(self)
22421901, 12472350, 8844473, 6852337, 5513520, 13065414, 4706611, 5732063, 11627544, 3076536, 25047700, 12472350, ss221098716, ss232515070, ss239780103, ss651525664, ss980450038, ss1071787085, ss1310979706, ss1429982689, ss1580687398, ss1610736149, ss1653730182, ss1923690133, ss1969816812, ss2022431008, ss2150560182, ss2706037068, ss2812853958, ss2995210417, ss3345861779, ss3663106225, ss3731421746, ss3762167048, ss3784801941, ss3790246607, ss3795122011, ss3828703511, ss3837792830, ss3859610564, ss3905888020, ss5167078393, ss5507641450, ss5635665546, ss5844424157, ss5964056220	NC_000004.11:100158022:T:G	NC_000004.12:99236865:T:G	(self)
29482181, 158832672, 35646683, 462016407, 12145950270, ss2265424770, ss3024990769, ss3647802614, ss3712656741, ss3805315469, ss3843231221, ss4624638851, ss5260288444, ss5458930882, ss5541956246, ss5701809579, ss5805353979, ss5854355956, ss5864676969	NC_000004.12:99236865:T:G	NC_000004.12:99236865:T:G	(self)
ss22213752	NT_016354.16:24652726:T:G	NC_000004.12:99236865:T:G	(self)
ss2326279, ss42171909, ss135207923	NT_016354.19:24705743:T:G	NC_000004.12:99236865: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 rs1497378

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
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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

rs1497378