Name: rs7678074
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.

rs7678074

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:99258085 (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: G>A / G>C
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.397918 (105325/264690, TOPMED)
A=0.404178 (56572/139968, GnomAD)
A=0.09665 (2731/28258, 14KJPN) (+ 14 more)
A=0.41831 (7609/18190, ALFA)
A=0.09302 (1559/16760, 8.3KJPN)
A=0.3140 (2011/6404, 1000G_30x)
A=0.3033 (1519/5008, 1000G)
A=0.4442 (1990/4480, Estonian)
A=0.4683 (1805/3854, ALSPAC)
A=0.4830 (1791/3708, TWINSUK)
A=0.1400 (409/2922, KOREAN)
A=0.450 (449/998, GoNL)
A=0.487 (292/600, NorthernSweden)
G=0.388 (118/304, SGDP_PRJ)
A=0.380 (82/216, Qatari)
A=0.075 (16/212, Vietnamese)
G=0.29 (12/42, Siberian)

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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	18190	G=0.58169	A=0.41831, C=0.00000
European	Sub	13808	G=0.54309	A=0.45691, C=0.00000
African	Sub	2728	G=0.7815	A=0.2185, C=0.0000
African Others	Sub	102	G=0.784	A=0.216, C=0.000
African American	Sub	2626	G=0.7814	A=0.2186, C=0.0000
Asian	Sub	112	G=0.920	A=0.080, C=0.000
East Asian	Sub	86	G=0.92	A=0.08, C=0.00
Other Asian	Sub	26	G=0.92	A=0.08, C=0.00
Latin American 1	Sub	146	G=0.500	A=0.500, C=0.000
Latin American 2	Sub	610	G=0.489	A=0.511, C=0.000
South Asian	Sub	98	G=0.83	A=0.17, C=0.00
Other	Sub	688	G=0.574	A=0.426, C=0.000

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	G=0.602082	A=0.397918
gnomAD - Genomes	Global	Study-wide	139968	G=0.595822	A=0.404178
gnomAD - Genomes	European	Sub	75814	G=0.53137	A=0.46863
gnomAD - Genomes	African	Sub	41936	G=0.73989	A=0.26011
gnomAD - Genomes	American	Sub	13630	G=0.48687	A=0.51313
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	G=0.4512	A=0.5488
gnomAD - Genomes	East Asian	Sub	3118	G=0.8708	A=0.1292
gnomAD - Genomes	Other	Sub	2150	G=0.5740	A=0.4260
14KJPN	JAPANESE	Study-wide	28258	G=0.90335	A=0.09665
Allele Frequency Aggregator	Total	Global	18190	G=0.58169	A=0.41831, C=0.00000
Allele Frequency Aggregator	European	Sub	13808	G=0.54309	A=0.45691, C=0.00000
Allele Frequency Aggregator	African	Sub	2728	G=0.7815	A=0.2185, C=0.0000
Allele Frequency Aggregator	Other	Sub	688	G=0.574	A=0.426, C=0.000
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.489	A=0.511, C=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.500	A=0.500, C=0.000
Allele Frequency Aggregator	Asian	Sub	112	G=0.920	A=0.080, C=0.000
Allele Frequency Aggregator	South Asian	Sub	98	G=0.83	A=0.17, C=0.00
8.3KJPN	JAPANESE	Study-wide	16760	G=0.90698	A=0.09302
1000Genomes_30x	Global	Study-wide	6404	G=0.6860	A=0.3140
1000Genomes_30x	African	Sub	1786	G=0.7464	A=0.2536
1000Genomes_30x	Europe	Sub	1266	G=0.5016	A=0.4984
1000Genomes_30x	South Asian	Sub	1202	G=0.8261	A=0.1739
1000Genomes_30x	East Asian	Sub	1170	G=0.8667	A=0.1333
1000Genomes_30x	American	Sub	980	G=0.427	A=0.573
1000Genomes	Global	Study-wide	5008	G=0.6967	A=0.3033
1000Genomes	African	Sub	1322	G=0.7489	A=0.2511
1000Genomes	East Asian	Sub	1008	G=0.8750	A=0.1250
1000Genomes	Europe	Sub	1006	G=0.5040	A=0.4960
1000Genomes	South Asian	Sub	978	G=0.829	A=0.171
1000Genomes	American	Sub	694	G=0.431	A=0.569
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.5558	A=0.4442
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.5317	A=0.4683
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.5170	A=0.4830
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.8600	A=0.1400
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.550	A=0.450
Northern Sweden	ACPOP	Study-wide	600	G=0.513	A=0.487
SGDP_PRJ	Global	Study-wide	304	G=0.388	A=0.612
Qatari	Global	Study-wide	216	G=0.620	A=0.380
A Vietnamese Genetic Variation Database	Global	Study-wide	212	G=0.925	A=0.075
Siberian	Global	Study-wide	42	G=0.29	A=0.71

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.99258085G>A
GRCh38.p14 chr 4	NC_000004.12:g.99258085G>C
GRCh37.p13 chr 4	NC_000004.11:g.100179242G>A
GRCh37.p13 chr 4	NC_000004.11:g.100179242G>C

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	G=	A	C
GRCh38.p14 chr 4	NC_000004.12:g.99258085=	NC_000004.12:g.99258085G>A	NC_000004.12:g.99258085G>C
GRCh37.p13 chr 4	NC_000004.11:g.100179242=	NC_000004.11:g.100179242G>A	NC_000004.11:g.100179242G>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#.

53 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss11655406	Jul 11, 2003 (116)
2	SSAHASNP	ss22206178	Apr 05, 2004 (121)
3	BL	ss253372138	May 09, 2011 (134)
4	GMI	ss277844421	May 04, 2012 (137)
5	PJP	ss293147516	May 09, 2011 (134)
6	1000GENOMES	ss331832183	May 09, 2011 (134)
7	TISHKOFF	ss557721195	Apr 25, 2013 (138)
8	SSMP	ss651525741	Apr 25, 2013 (138)
9	EVA-GONL	ss980450215	Aug 21, 2014 (142)
10	JMKIDD_LAB	ss1071787197	Aug 21, 2014 (142)
11	1000GENOMES	ss1310980250	Aug 21, 2014 (142)
12	DDI	ss1429982743	Apr 01, 2015 (144)
13	EVA_DECODE	ss1589954250	Apr 01, 2015 (144)
14	EVA_UK10K_ALSPAC	ss1610736496	Apr 01, 2015 (144)
15	EVA_UK10K_TWINSUK	ss1653730529	Apr 01, 2015 (144)
16	HAMMER_LAB	ss1801909849	Sep 08, 2015 (146)
17	WEILL_CORNELL_DGM	ss1923690270	Feb 12, 2016 (147)
18	JJLAB	ss2022431093	Sep 14, 2016 (149)
19	USC_VALOUEV	ss2150560267	Dec 20, 2016 (150)
20	HUMAN_LONGEVITY	ss2265426094	Dec 20, 2016 (150)
21	GRF	ss2706037129	Nov 08, 2017 (151)
22	GNOMAD	ss2812855677	Nov 08, 2017 (151)
23	AFFY	ss2985926700	Nov 08, 2017 (151)
24	SWEGEN	ss2995210657	Nov 08, 2017 (151)
25	BIOINF_KMB_FNS_UNIBA	ss3024990817	Nov 08, 2017 (151)
26	CSHL	ss3345861851	Nov 08, 2017 (151)
27	URBANLAB	ss3647802661	Oct 12, 2018 (152)
28	EGCUT_WGS	ss3663106482	Jul 13, 2019 (153)
29	EVA_DECODE	ss3712657027	Jul 13, 2019 (153)
30	ACPOP	ss3731421887	Jul 13, 2019 (153)
31	EVA	ss3762167181	Jul 13, 2019 (153)
32	PACBIO	ss3784801988	Jul 13, 2019 (153)
33	PACBIO	ss3790246647	Jul 13, 2019 (153)
34	PACBIO	ss3795122051	Jul 13, 2019 (153)
35	KHV_HUMAN_GENOMES	ss3805315611	Jul 13, 2019 (153)
36	EVA	ss3828703595	Apr 26, 2020 (154)
37	EVA	ss3837792880	Apr 26, 2020 (154)
38	EVA	ss3843231273	Apr 26, 2020 (154)
39	SGDP_PRJ	ss3859610835	Apr 26, 2020 (154)
40	KRGDB	ss3905888376	Apr 26, 2020 (154)
41	TOPMED	ss4624644254	Apr 26, 2021 (155)
42	TOMMO_GENOMICS	ss5167078931	Apr 26, 2021 (155)
43	1000G_HIGH_COVERAGE	ss5260288871	Oct 13, 2022 (156)
44	HUGCELL_USP	ss5458931266	Oct 13, 2022 (156)
45	EVA	ss5507641529	Oct 13, 2022 (156)
46	1000G_HIGH_COVERAGE	ss5541956958	Oct 13, 2022 (156)
47	SANFORD_IMAGENETICS	ss5635665811	Oct 13, 2022 (156)
48	TOMMO_GENOMICS	ss5701810301	Oct 13, 2022 (156)
49	YY_MCH	ss5805354083	Oct 13, 2022 (156)
50	EVA	ss5844424366	Oct 13, 2022 (156)
51	EVA	ss5854356021	Oct 13, 2022 (156)
52	EVA	ss5864677502	Oct 13, 2022 (156)
53	EVA	ss5964056519	Oct 13, 2022 (156)
54	1000Genomes	NC_000004.11 - 100179242	Oct 12, 2018 (152)
55	1000Genomes_30x	NC_000004.12 - 99258085	Oct 13, 2022 (156)
56	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 100179242	Oct 12, 2018 (152)
57	Genetic variation in the Estonian population	NC_000004.11 - 100179242	Oct 12, 2018 (152)
58	gnomAD - Genomes	NC_000004.12 - 99258085	Apr 26, 2021 (155)
59	Genome of the Netherlands Release 5	NC_000004.11 - 100179242	Apr 26, 2020 (154)
60	KOREAN population from KRGDB	NC_000004.11 - 100179242	Apr 26, 2020 (154)
61	Northern Sweden	NC_000004.11 - 100179242	Jul 13, 2019 (153)
62	Qatari	NC_000004.11 - 100179242	Apr 26, 2020 (154)
63	SGDP_PRJ	NC_000004.11 - 100179242	Apr 26, 2020 (154)
64	Siberian	NC_000004.11 - 100179242	Apr 26, 2020 (154)
65	8.3KJPN	NC_000004.11 - 100179242	Apr 26, 2021 (155)
66	14KJPN	NC_000004.12 - 99258085	Oct 13, 2022 (156)
67	TopMed	NC_000004.12 - 99258085	Apr 26, 2021 (155)
68	UK 10K study - Twins	NC_000004.11 - 100179242	Oct 12, 2018 (152)
69	A Vietnamese Genetic Variation Database	NC_000004.11 - 100179242	Jul 13, 2019 (153)
70	ALFA	NC_000004.12 - 99258085	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)
rs35634797	May 23, 2006 (127)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss253372138, ss277844421, ss293147516, ss1589954250	NC_000004.10:100398264:G:A	NC_000004.12:99258084:G:A	(self)
22422458, 12472732, 8844730, 5513697, 13065770, 4706752, 5732200, 11627815, 3076621, 25048238, 12472732, 2744388, ss331832183, ss557721195, ss651525741, ss980450215, ss1071787197, ss1310980250, ss1429982743, ss1610736496, ss1653730529, ss1801909849, ss1923690270, ss2022431093, ss2150560267, ss2706037129, ss2812855677, ss2985926700, ss2995210657, ss3345861851, ss3663106482, ss3731421887, ss3762167181, ss3784801988, ss3790246647, ss3795122051, ss3828703595, ss3837792880, ss3859610835, ss3905888376, ss5167078931, ss5507641529, ss5635665811, ss5844424366, ss5964056519	NC_000004.11:100179241:G:A	NC_000004.12:99258084:G:A	(self)
29482893, 158836890, 35647405, 462021810, 7544138399, ss2265426094, ss3024990817, ss3647802661, ss3712657027, ss3805315611, ss3843231273, ss4624644254, ss5260288871, ss5458931266, ss5541956958, ss5701810301, ss5805354083, ss5854356021, ss5864677502	NC_000004.12:99258084:G:A	NC_000004.12:99258084:G:A	(self)
ss11655406	NT_016354.15:24673945:G:A	NC_000004.12:99258084:G:A	(self)
ss22206178	NT_016354.16:24673945:G:A	NC_000004.12:99258084:G:A	(self)
7544138399	NC_000004.12:99258084:G:C	NC_000004.12:99258084:G: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 rs7678074

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

rs7678074