Name: rs12567084
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.

rs12567084

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:227581028 (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=0.014991 (3968/264690, TOPMED)
T=0.015817 (2210/139722, GnomAD)
T=0.01522 (430/28256, 14KJPN) (+ 15 more)
T=0.01027 (194/18890, ALFA)
T=0.01521 (255/16760, 8.3KJPN)
T=0.0289 (185/6404, 1000G_30x)
T=0.0304 (152/5008, 1000G)
T=0.0096 (43/4480, Estonian)
T=0.0253 (74/2922, KOREAN)
T=0.0235 (43/1832, Korea1K)
T=0.005 (3/600, NorthernSweden)
T=0.000 (0/320, HapMap)
T=0.014 (3/216, Qatari)
T=0.029 (6/210, Vietnamese)
C=0.50 (20/40, SGDP_PRJ)
T=0.50 (20/40, SGDP_PRJ)
C=0.50 (9/18, Siberian)
T=0.50 (9/18, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ZNF678 : 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	18890	C=0.98973	T=0.01027
European	Sub	14286	C=0.99685	T=0.00315
African	Sub	2946	C=0.9566	T=0.0434
African Others	Sub	114	C=0.956	T=0.044
African American	Sub	2832	C=0.9566	T=0.0434
Asian	Sub	112	C=0.982	T=0.018
East Asian	Sub	86	C=0.99	T=0.01
Other Asian	Sub	26	C=0.96	T=0.04
Latin American 1	Sub	146	C=1.000	T=0.000
Latin American 2	Sub	610	C=1.000	T=0.000
South Asian	Sub	98	C=0.96	T=0.04
Other	Sub	692	C=0.978	T=0.022

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=0.985009	T=0.014991
gnomAD - Genomes	Global	Study-wide	139722	C=0.984183	T=0.015817
gnomAD - Genomes	European	Sub	75692	C=0.99658	T=0.00342
gnomAD - Genomes	African	Sub	41812	C=0.95666	T=0.04334
gnomAD - Genomes	American	Sub	13612	C=0.99772	T=0.00228
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.9967	T=0.0033
gnomAD - Genomes	East Asian	Sub	3132	C=0.9802	T=0.0198
gnomAD - Genomes	Other	Sub	2150	C=0.9837	T=0.0163
14KJPN	JAPANESE	Study-wide	28256	C=0.98478	T=0.01522
Allele Frequency Aggregator	Total	Global	18890	C=0.98973	T=0.01027
Allele Frequency Aggregator	European	Sub	14286	C=0.99685	T=0.00315
Allele Frequency Aggregator	African	Sub	2946	C=0.9566	T=0.0434
Allele Frequency Aggregator	Other	Sub	692	C=0.978	T=0.022
Allele Frequency Aggregator	Latin American 2	Sub	610	C=1.000	T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	C=1.000	T=0.000
Allele Frequency Aggregator	Asian	Sub	112	C=0.982	T=0.018
Allele Frequency Aggregator	South Asian	Sub	98	C=0.96	T=0.04
8.3KJPN	JAPANESE	Study-wide	16760	C=0.98479	T=0.01521
1000Genomes_30x	Global	Study-wide	6404	C=0.9711	T=0.0289
1000Genomes_30x	African	Sub	1786	C=0.9614	T=0.0386
1000Genomes_30x	Europe	Sub	1266	C=0.9992	T=0.0008
1000Genomes_30x	South Asian	Sub	1202	C=0.9368	T=0.0632
1000Genomes_30x	East Asian	Sub	1170	C=0.9692	T=0.0308
1000Genomes_30x	American	Sub	980	C=0.997	T=0.003
1000Genomes	Global	Study-wide	5008	C=0.9696	T=0.0304
1000Genomes	African	Sub	1322	C=0.9584	T=0.0416
1000Genomes	East Asian	Sub	1008	C=0.9683	T=0.0317
1000Genomes	Europe	Sub	1006	C=0.9990	T=0.0010
1000Genomes	South Asian	Sub	978	C=0.937	T=0.063
1000Genomes	American	Sub	694	C=0.997	T=0.003
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9904	T=0.0096
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9747	T=0.0253
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9765	T=0.0235
Northern Sweden	ACPOP	Study-wide	600	C=0.995	T=0.005
HapMap	Global	Study-wide	320	C=1.000	T=0.000
HapMap	American	Sub	116	C=1.000	T=0.000
HapMap	African	Sub	114	C=1.000	T=0.000
HapMap	Asian	Sub	90	C=1.00	T=0.00
Qatari	Global	Study-wide	216	C=0.986	T=0.014
A Vietnamese Genetic Variation Database	Global	Study-wide	210	C=0.971	T=0.029
SGDP_PRJ	Global	Study-wide	40	C=0.50	T=0.50
Siberian	Global	Study-wide	18	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.227581028C>T
GRCh37.p13 chr 1	NC_000001.10:g.227768729C>T

Gene: ZNF678, zinc finger protein 678 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ZNF678 transcript variant 2	NM_001367909.1:c.-164+173… NM_001367909.1:c.-164+17304C>T	N/A	Intron Variant
ZNF678 transcript variant 4	NM_001367910.1:c.-256-148… NM_001367910.1:c.-256-1486C>T	N/A	Intron Variant
ZNF678 transcript variant 5	NM_001367911.1:c.30+17304… NM_001367911.1:c.30+17304C>T	N/A	Intron Variant
ZNF678 transcript variant 1	NM_178549.4:c.31-1486C>T	N/A	Intron Variant
ZNF678 transcript variant 3	NR_102302.2: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.227581028=	NC_000001.11:g.227581028C>T
GRCh37.p13 chr 1	NC_000001.10:g.227768729=	NC_000001.10:g.227768729C>T
ZNF678 transcript variant 2	NM_001367909.1:c.-164+17304=	NM_001367909.1:c.-164+17304C>T
ZNF678 transcript variant 4	NM_001367910.1:c.-256-1486=	NM_001367910.1:c.-256-1486C>T
ZNF678 transcript variant 5	NM_001367911.1:c.30+17304=	NM_001367911.1:c.30+17304C>T
ZNF678 transcript variant 1	NM_178549.3:c.31-1486=	NM_178549.3:c.31-1486C>T
ZNF678 transcript variant 1	NM_178549.4:c.31-1486=	NM_178549.4:c.31-1486C>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#.

37 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	CSHL-HAPMAP	ss19860451	Feb 28, 2004 (120)
2	ABI	ss41291872	Mar 15, 2006 (126)
3	1000GENOMES	ss111882875	Jan 25, 2009 (130)
4	ENSEMBL	ss161225358	Dec 01, 2009 (131)
5	COMPLETE_GENOMICS	ss165324345	Jul 04, 2010 (132)
6	1000GENOMES	ss218921180	Jul 14, 2010 (132)
7	TISHKOFF	ss555184280	Apr 25, 2013 (138)
8	SSMP	ss648757268	Apr 25, 2013 (138)
9	JMKIDD_LAB	ss1068660761	Aug 21, 2014 (142)
10	1000GENOMES	ss1294944903	Aug 21, 2014 (142)
11	EVA_DECODE	ss1585621564	Apr 01, 2015 (144)
12	WEILL_CORNELL_DGM	ss1919444625	Feb 12, 2016 (147)
13	USC_VALOUEV	ss2148282688	Dec 20, 2016 (150)
14	HUMAN_LONGEVITY	ss2170696512	Dec 20, 2016 (150)
15	GRF	ss2698280887	Nov 08, 2017 (151)
16	GNOMAD	ss2767060440	Nov 08, 2017 (151)
17	SWEGEN	ss2988573996	Nov 08, 2017 (151)
18	EGCUT_WGS	ss3656532388	Jul 12, 2019 (153)
19	ACPOP	ss3727928161	Jul 12, 2019 (153)
20	EVA	ss3747428614	Jul 12, 2019 (153)
21	KHV_HUMAN_GENOMES	ss3800431411	Jul 12, 2019 (153)
22	SGDP_PRJ	ss3851052107	Apr 25, 2020 (154)
23	KRGDB	ss3896392394	Apr 25, 2020 (154)
24	KOGIC	ss3946645219	Apr 25, 2020 (154)
25	TOPMED	ss4486189001	Apr 25, 2021 (155)
26	TOMMO_GENOMICS	ss5148774443	Apr 25, 2021 (155)
27	1000G_HIGH_COVERAGE	ss5246054638	Oct 12, 2022 (156)
28	EVA	ss5325261543	Oct 12, 2022 (156)
29	HUGCELL_USP	ss5446464287	Oct 12, 2022 (156)
30	EVA	ss5506216906	Oct 12, 2022 (156)
31	1000G_HIGH_COVERAGE	ss5520282765	Oct 12, 2022 (156)
32	SANFORD_IMAGENETICS	ss5627593745	Oct 12, 2022 (156)
33	TOMMO_GENOMICS	ss5676632605	Oct 12, 2022 (156)
34	YY_MCH	ss5801705792	Oct 12, 2022 (156)
35	EVA	ss5849319083	Oct 12, 2022 (156)
36	EVA	ss5912269972	Oct 12, 2022 (156)
37	EVA	ss5939439004	Oct 12, 2022 (156)
38	1000Genomes	NC_000001.10 - 227768729	Oct 11, 2018 (152)
39	1000Genomes_30x	NC_000001.11 - 227581028	Oct 12, 2022 (156)
40	Genetic variation in the Estonian population	NC_000001.10 - 227768729	Oct 11, 2018 (152)
41	gnomAD - Genomes	NC_000001.11 - 227581028	Apr 25, 2021 (155)
42	HapMap	NC_000001.11 - 227581028	Apr 25, 2020 (154)
43	KOREAN population from KRGDB	NC_000001.10 - 227768729	Apr 25, 2020 (154)
44	Korean Genome Project	NC_000001.11 - 227581028	Apr 25, 2020 (154)
45	Northern Sweden	NC_000001.10 - 227768729	Jul 12, 2019 (153)
46	Qatari	NC_000001.10 - 227768729	Apr 25, 2020 (154)
47	SGDP_PRJ	NC_000001.10 - 227768729	Apr 25, 2020 (154)
48	Siberian	NC_000001.10 - 227768729	Apr 25, 2020 (154)
49	8.3KJPN	NC_000001.10 - 227768729	Apr 25, 2021 (155)
50	14KJPN	NC_000001.11 - 227581028	Oct 12, 2022 (156)
51	TopMed	NC_000001.11 - 227581028	Apr 25, 2021 (155)
52	A Vietnamese Genetic Variation Database	NC_000001.10 - 227768729	Jul 12, 2019 (153)
53	ALFA	NC_000001.11 - 227581028	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
ss111882875, ss165324345, ss1585621564	NC_000001.9:225835351:C:T	NC_000001.11:227581027:C:T	(self)
5810345, 2270636, 3569788, 1213026, 1486555, 3069087, 799042, 6743750, 698590, ss218921180, ss555184280, ss648757268, ss1068660761, ss1294944903, ss1919444625, ss2148282688, ss2698280887, ss2767060440, ss2988573996, ss3656532388, ss3727928161, ss3747428614, ss3851052107, ss3896392394, ss5148774443, ss5325261543, ss5506216906, ss5627593745, ss5939439004	NC_000001.10:227768728:C:T	NC_000001.11:227581027:C:T	(self)
7808700, 41728531, 284079, 3023220, 10469709, 49795336, 14328201876, ss2170696512, ss3800431411, ss3946645219, ss4486189001, ss5246054638, ss5446464287, ss5520282765, ss5676632605, ss5801705792, ss5849319083, ss5912269972	NC_000001.11:227581027:C:T	NC_000001.11:227581027:C:T	(self)
ss19860451	NT_004559.11:3944922:C:T	NC_000001.11:227581027:C:T	(self)
ss41291872, ss161225358	NT_167186.1:21286507:C:T	NC_000001.11:227581027: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 rs12567084

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

rs12567084