Name: rs78943400
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.

rs78943400

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr17:47166540 (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: A>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.073346 (19414/264690, TOPMED)
G=0.074117 (10377/140008, GnomAD)
G=0.13703 (3872/28256, 14KJPN) (+ 16 more)
G=0.08878 (1677/18890, ALFA)
G=0.13747 (2304/16760, 8.3KJPN)
G=0.1051 (673/6404, 1000G_30x)
G=0.1072 (537/5008, 1000G)
G=0.1203 (539/4480, Estonian)
G=0.0924 (356/3854, ALSPAC)
G=0.0917 (340/3708, TWINSUK)
G=0.1573 (461/2930, KOREAN)
G=0.1485 (272/1832, Korea1K)
G=0.099 (99/998, GoNL)
G=0.090 (54/600, NorthernSweden)
G=0.060 (13/216, Qatari)
G=0.222 (47/212, Vietnamese)
A=0.462 (49/106, SGDP_PRJ)
G=0.10 (4/40, GENOME_DK)
A=0.3 (2/6, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CDC27 : 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	A=0.91122	G=0.08878
European	Sub	14286	A=0.89969	G=0.10031
African	Sub	2946	A=0.9711	G=0.0289
African Others	Sub	114	A=1.000	G=0.000
African American	Sub	2832	A=0.9700	G=0.0300
Asian	Sub	112	A=0.786	G=0.214
East Asian	Sub	86	A=0.77	G=0.23
Other Asian	Sub	26	A=0.85	G=0.15
Latin American 1	Sub	146	A=0.966	G=0.034
Latin American 2	Sub	610	A=0.928	G=0.072
South Asian	Sub	98	A=0.85	G=0.15
Other	Sub	692	A=0.897	G=0.103

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	A=0.926654	G=0.073346
gnomAD - Genomes	Global	Study-wide	140008	A=0.925883	G=0.074117
gnomAD - Genomes	European	Sub	75790	A=0.90802	G=0.09198
gnomAD - Genomes	African	Sub	41996	A=0.97443	G=0.02557
gnomAD - Genomes	American	Sub	13628	A=0.90820	G=0.09180
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	A=0.9175	G=0.0825
gnomAD - Genomes	East Asian	Sub	3130	A=0.7994	G=0.2006
gnomAD - Genomes	Other	Sub	2144	A=0.9165	G=0.0835
14KJPN	JAPANESE	Study-wide	28256	A=0.86297	G=0.13703
Allele Frequency Aggregator	Total	Global	18890	A=0.91122	G=0.08878
Allele Frequency Aggregator	European	Sub	14286	A=0.89969	G=0.10031
Allele Frequency Aggregator	African	Sub	2946	A=0.9711	G=0.0289
Allele Frequency Aggregator	Other	Sub	692	A=0.897	G=0.103
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.928	G=0.072
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.966	G=0.034
Allele Frequency Aggregator	Asian	Sub	112	A=0.786	G=0.214
Allele Frequency Aggregator	South Asian	Sub	98	A=0.85	G=0.15
8.3KJPN	JAPANESE	Study-wide	16760	A=0.86253	G=0.13747
1000Genomes_30x	Global	Study-wide	6404	A=0.8949	G=0.1051
1000Genomes_30x	African	Sub	1786	A=0.9826	G=0.0174
1000Genomes_30x	Europe	Sub	1266	A=0.9186	G=0.0814
1000Genomes_30x	South Asian	Sub	1202	A=0.8045	G=0.1955
1000Genomes_30x	East Asian	Sub	1170	A=0.8393	G=0.1607
1000Genomes_30x	American	Sub	980	A=0.882	G=0.118
1000Genomes	Global	Study-wide	5008	A=0.8928	G=0.1072
1000Genomes	African	Sub	1322	A=0.9826	G=0.0174
1000Genomes	East Asian	Sub	1008	A=0.8403	G=0.1597
1000Genomes	Europe	Sub	1006	A=0.9215	G=0.0785
1000Genomes	South Asian	Sub	978	A=0.793	G=0.207
1000Genomes	American	Sub	694	A=0.896	G=0.104
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.8797	G=0.1203
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.9076	G=0.0924
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.9083	G=0.0917
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.8427	G=0.1573
Korean Genome Project	KOREAN	Study-wide	1832	A=0.8515	G=0.1485
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.901	G=0.099
Northern Sweden	ACPOP	Study-wide	600	A=0.910	G=0.090
Qatari	Global	Study-wide	216	A=0.940	G=0.060
A Vietnamese Genetic Variation Database	Global	Study-wide	212	A=0.778	G=0.222
SGDP_PRJ	Global	Study-wide	106	A=0.462	G=0.538
The Danish reference pan genome	Danish	Study-wide	40	A=0.90	G=0.10
Siberian	Global	Study-wide	6	A=0.3	G=0.7

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 17	NC_000017.11:g.47166540A>G
GRCh37.p13 chr 17	NC_000017.10:g.45243906A>G

Gene: CDC27, cell division cycle 27 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CDC27 transcript variant 1	NM_001114091.4:c.377+3377… NM_001114091.4:c.377+3377T>C	N/A	Intron Variant
CDC27 transcript variant 2	NM_001256.6:c.377+3377T>C	N/A	Intron Variant
CDC27 transcript variant 3	NM_001293089.3:c.377+3377… NM_001293089.3:c.377+3377T>C	N/A	Intron Variant
CDC27 transcript variant 4	NM_001293091.3:c.194+3377… NM_001293091.3:c.194+3377T>C	N/A	Intron Variant
CDC27 transcript variant 5	NM_001353035.2:c.377+3377… NM_001353035.2:c.377+3377T>C	N/A	Intron Variant
CDC27 transcript variant 6	NM_001353047.2:c.377+3377… NM_001353047.2:c.377+3377T>C	N/A	Intron Variant
CDC27 transcript variant 7	NM_001353049.2:c.194+3377… NM_001353049.2:c.194+3377T>C	N/A	Intron Variant
CDC27 transcript variant 8	NM_001353050.2:c.69-8237T… NM_001353050.2:c.69-8237T>C	N/A	Intron Variant
CDC27 transcript variant 9	NM_001353051.2:c.-892-823… NM_001353051.2:c.-892-8237T>C	N/A	Intron Variant
CDC27 transcript variant 10	NR_148340.2:n.	N/A	Intron Variant
CDC27 transcript variant X1	XM_011525546.4:c.377+3377… XM_011525546.4:c.377+3377T>C	N/A	Intron Variant
CDC27 transcript variant X3	XM_011525547.4:c.377+3377… XM_011525547.4:c.377+3377T>C	N/A	Intron Variant
CDC27 transcript variant X4	XM_011525548.4:c.194+3377… XM_011525548.4:c.194+3377T>C	N/A	Intron Variant
CDC27 transcript variant X5	XM_011525549.3:c.194+3377… XM_011525549.3:c.194+3377T>C	N/A	Intron Variant
CDC27 transcript variant X7	XM_017025484.3:c.194+3377… XM_017025484.3:c.194+3377T>C	N/A	Intron Variant
CDC27 transcript variant X8	XM_017025485.3:c.69-8237T… XM_017025485.3:c.69-8237T>C	N/A	Intron Variant
CDC27 transcript variant X2	XM_047437229.1:c.377+3377… XM_047437229.1:c.377+3377T>C	N/A	Intron Variant
CDC27 transcript variant X6	XM_047437230.1:c.194+3377… XM_047437230.1:c.194+3377T>C	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	A=	G
GRCh38.p14 chr 17	NC_000017.11:g.47166540=	NC_000017.11:g.47166540A>G
GRCh37.p13 chr 17	NC_000017.10:g.45243906=	NC_000017.10:g.45243906A>G
CDC27 transcript variant 1	NM_001114091.1:c.377+3377=	NM_001114091.1:c.377+3377T>C
CDC27 transcript variant 1	NM_001114091.4:c.377+3377=	NM_001114091.4:c.377+3377T>C
CDC27 transcript variant 2	NM_001256.3:c.377+3377=	NM_001256.3:c.377+3377T>C
CDC27 transcript variant 2	NM_001256.6:c.377+3377=	NM_001256.6:c.377+3377T>C
CDC27 transcript variant 3	NM_001293089.3:c.377+3377=	NM_001293089.3:c.377+3377T>C
CDC27 transcript variant 4	NM_001293091.3:c.194+3377=	NM_001293091.3:c.194+3377T>C
CDC27 transcript variant 5	NM_001353035.2:c.377+3377=	NM_001353035.2:c.377+3377T>C
CDC27 transcript variant 6	NM_001353047.2:c.377+3377=	NM_001353047.2:c.377+3377T>C
CDC27 transcript variant 7	NM_001353049.2:c.194+3377=	NM_001353049.2:c.194+3377T>C
CDC27 transcript variant 8	NM_001353050.2:c.69-8237=	NM_001353050.2:c.69-8237T>C
CDC27 transcript variant 9	NM_001353051.2:c.-892-8237=	NM_001353051.2:c.-892-8237T>C
CDC27 transcript variant X1	XM_005257891.1:c.377+3377=	XM_005257891.1:c.377+3377T>C
CDC27 transcript variant X2	XM_005257892.1:c.377+3377=	XM_005257892.1:c.377+3377T>C
CDC27 transcript variant X3	XM_005257893.1:c.194+3377=	XM_005257893.1:c.194+3377T>C
CDC27 transcript variant X4	XM_005257894.1:c.194+3377=	XM_005257894.1:c.194+3377T>C
CDC27 transcript variant X5	XM_005257895.1:c.194+3377=	XM_005257895.1:c.194+3377T>C
CDC27 transcript variant X6	XM_005257896.1:c.229+3377=	XM_005257896.1:c.229+3377T>C
CDC27 transcript variant X7	XM_005257897.1:c.70+3377=	XM_005257897.1:c.70+3377T>C
CDC27 transcript variant X1	XM_011525546.4:c.377+3377=	XM_011525546.4:c.377+3377T>C
CDC27 transcript variant X3	XM_011525547.4:c.377+3377=	XM_011525547.4:c.377+3377T>C
CDC27 transcript variant X4	XM_011525548.4:c.194+3377=	XM_011525548.4:c.194+3377T>C
CDC27 transcript variant X5	XM_011525549.3:c.194+3377=	XM_011525549.3:c.194+3377T>C
CDC27 transcript variant X7	XM_017025484.3:c.194+3377=	XM_017025484.3:c.194+3377T>C
CDC27 transcript variant X8	XM_017025485.3:c.69-8237=	XM_017025485.3:c.69-8237T>C
CDC27 transcript variant X2	XM_047437229.1:c.377+3377=	XM_047437229.1:c.377+3377T>C
CDC27 transcript variant X6	XM_047437230.1:c.194+3377=	XM_047437230.1:c.194+3377T>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#.

52 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GMI	ss158058926	Dec 01, 2009 (131)
2	1000GENOMES	ss237253793	Jul 15, 2010 (132)
3	1000GENOMES	ss243547798	Jul 15, 2010 (132)
4	GMI	ss282775333	May 04, 2012 (137)
5	TISHKOFF	ss565288731	Apr 25, 2013 (138)
6	SSMP	ss661094870	Apr 25, 2013 (138)
7	EVA-GONL	ss993137280	Aug 21, 2014 (142)
8	JMKIDD_LAB	ss1081077420	Aug 21, 2014 (142)
9	1000GENOMES	ss1358771022	Aug 21, 2014 (142)
10	DDI	ss1428040128	Apr 01, 2015 (144)
11	EVA_GENOME_DK	ss1578169011	Apr 01, 2015 (144)
12	EVA_UK10K_ALSPAC	ss1635706248	Apr 01, 2015 (144)
13	EVA_UK10K_TWINSUK	ss1678700281	Apr 01, 2015 (144)
14	EVA_DECODE	ss1697179837	Apr 01, 2015 (144)
15	WEILL_CORNELL_DGM	ss1936599625	Feb 12, 2016 (147)
16	GENOMED	ss1968395309	Jul 19, 2016 (147)
17	JJLAB	ss2029076151	Sep 14, 2016 (149)
18	USC_VALOUEV	ss2157549908	Dec 20, 2016 (150)
19	HUMAN_LONGEVITY	ss2217059020	Dec 20, 2016 (150)
20	SYSTEMSBIOZJU	ss2629033166	Nov 08, 2017 (151)
21	GRF	ss2702109658	Nov 08, 2017 (151)
22	GNOMAD	ss2950231666	Nov 08, 2017 (151)
23	SWEGEN	ss3015588738	Nov 08, 2017 (151)
24	ILLUMINA	ss3021784363	Nov 08, 2017 (151)
25	BIOINF_KMB_FNS_UNIBA	ss3028359572	Nov 08, 2017 (151)
26	CSHL	ss3351756683	Nov 08, 2017 (151)
27	ILLUMINA	ss3625714152	Oct 12, 2018 (152)
28	ILLUMINA	ss3652201275	Oct 12, 2018 (152)
29	EGCUT_WGS	ss3682464540	Jul 13, 2019 (153)
30	EVA_DECODE	ss3700527067	Jul 13, 2019 (153)
31	ILLUMINA	ss3725625338	Jul 13, 2019 (153)
32	ACPOP	ss3742051946	Jul 13, 2019 (153)
33	EVA	ss3754702118	Jul 13, 2019 (153)
34	KHV_HUMAN_GENOMES	ss3819969881	Jul 13, 2019 (153)
35	EVA	ss3834883225	Apr 27, 2020 (154)
36	SGDP_PRJ	ss3885815832	Apr 27, 2020 (154)
37	KRGDB	ss3935519021	Apr 27, 2020 (154)
38	KOGIC	ss3978895232	Apr 27, 2020 (154)
39	TOPMED	ss5037002600	Apr 26, 2021 (155)
40	TOMMO_GENOMICS	ss5222570974	Apr 26, 2021 (155)
41	1000G_HIGH_COVERAGE	ss5303241752	Oct 16, 2022 (156)
42	EVA	ss5427783168	Oct 16, 2022 (156)
43	HUGCELL_USP	ss5496279263	Oct 16, 2022 (156)
44	EVA	ss5511775470	Oct 16, 2022 (156)
45	1000G_HIGH_COVERAGE	ss5607013251	Oct 16, 2022 (156)
46	SANFORD_IMAGENETICS	ss5660163341	Oct 16, 2022 (156)
47	TOMMO_GENOMICS	ss5778831294	Oct 16, 2022 (156)
48	YY_MCH	ss5816566276	Oct 16, 2022 (156)
49	EVA	ss5834026369	Oct 16, 2022 (156)
50	EVA	ss5851817836	Oct 16, 2022 (156)
51	EVA	ss5914050256	Oct 16, 2022 (156)
52	EVA	ss5951551772	Oct 16, 2022 (156)
53	1000Genomes	NC_000017.10 - 45243906	Oct 12, 2018 (152)
54	1000Genomes_30x	NC_000017.11 - 47166540	Oct 16, 2022 (156)
55	The Avon Longitudinal Study of Parents and Children	NC_000017.10 - 45243906	Oct 12, 2018 (152)
56	Genetic variation in the Estonian population	NC_000017.10 - 45243906	Oct 12, 2018 (152)
57	The Danish reference pan genome	NC_000017.10 - 45243906	Apr 27, 2020 (154)
58	gnomAD - Genomes	NC_000017.11 - 47166540	Apr 26, 2021 (155)
59	Genome of the Netherlands Release 5	NC_000017.10 - 45243906	Apr 27, 2020 (154)
60	KOREAN population from KRGDB	NC_000017.10 - 45243906	Apr 27, 2020 (154)
61	Korean Genome Project	NC_000017.11 - 47166540	Apr 27, 2020 (154)
62	Northern Sweden	NC_000017.10 - 45243906	Jul 13, 2019 (153)
63	Qatari	NC_000017.10 - 45243906	Apr 27, 2020 (154)
64	SGDP_PRJ	NC_000017.10 - 45243906	Apr 27, 2020 (154)
65	Siberian	NC_000017.10 - 45243906	Apr 27, 2020 (154)
66	8.3KJPN	NC_000017.10 - 45243906	Apr 26, 2021 (155)
67	14KJPN	NC_000017.11 - 47166540	Oct 16, 2022 (156)
68	TopMed	NC_000017.11 - 47166540	Apr 26, 2021 (155)
69	UK 10K study - Twins	NC_000017.10 - 45243906	Oct 12, 2018 (152)
70	A Vietnamese Genetic Variation Database	NC_000017.10 - 45243906	Jul 13, 2019 (153)
71	ALFA	NC_000017.11 - 47166540	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss282775333, ss1697179837	NC_000017.9:42598904:A:G	NC_000017.11:47166539:A:G	(self)
72017311, 39908662, 28202788, 4370872, 17787516, 42696415, 15336811, 18641547, 37832812, 10066262, 80540281, 39908662, 8828613, ss237253793, ss243547798, ss565288731, ss661094870, ss993137280, ss1081077420, ss1358771022, ss1428040128, ss1578169011, ss1635706248, ss1678700281, ss1936599625, ss1968395309, ss2029076151, ss2157549908, ss2629033166, ss2702109658, ss2950231666, ss3015588738, ss3021784363, ss3351756683, ss3625714152, ss3652201275, ss3682464540, ss3742051946, ss3754702118, ss3834883225, ss3885815832, ss3935519021, ss5222570974, ss5427783168, ss5511775470, ss5660163341, ss5834026369, ss5951551772	NC_000017.10:45243905:A:G	NC_000017.11:47166539:A:G	(self)
94539186, 508149569, 35273233, 112668398, 252548262, 481161496, ss2217059020, ss3028359572, ss3700527067, ss3725625338, ss3819969881, ss3978895232, ss5037002600, ss5303241752, ss5496279263, ss5607013251, ss5778831294, ss5816566276, ss5851817836, ss5914050256	NC_000017.11:47166539:A:G	NC_000017.11:47166539:A:G	(self)
ss158058926	NT_010783.15:10518057:A:G	NC_000017.11:47166539:A: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 rs78943400

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

rs78943400