Name: rs7548466
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.

rs7548466

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:100354272 (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=0.068034 (18008/264690, TOPMED)
T=0.061302 (8594/140192, GnomAD)
T=0.03892 (1816/46658, ALFA) (+ 17 more)
T=0.07616 (2152/28256, 14KJPN)
T=0.07416 (1243/16760, 8.3KJPN)
T=0.0845 (541/6404, 1000G_30x)
T=0.0805 (403/5008, 1000G)
T=0.0179 (80/4480, Estonian)
T=0.0202 (78/3854, ALSPAC)
T=0.0167 (62/3708, TWINSUK)
T=0.0832 (243/2922, KOREAN)
T=0.023 (23/998, GoNL)
T=0.040 (24/600, NorthernSweden)
T=0.086 (28/326, HapMap)
T=0.130 (28/216, Qatari)
T=0.079 (17/214, Vietnamese)
C=0.37 (31/84, SGDP_PRJ)
T=0.05 (2/40, GENOME_DK)
C=0.5 (1/2, Siberian)
T=0.5 (1/2, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CDC14A : 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	46658	C=0.96108	T=0.03892
European	Sub	32398	C=0.97889	T=0.02111
African	Sub	4938	C=0.8657	T=0.1343
African Others	Sub	180	C=0.822	T=0.178
African American	Sub	4758	C=0.8674	T=0.1326
Asian	Sub	438	C=0.886	T=0.114
East Asian	Sub	372	C=0.898	T=0.102
Other Asian	Sub	66	C=0.82	T=0.18
Latin American 1	Sub	574	C=0.929	T=0.071
Latin American 2	Sub	4902	C=0.9506	T=0.0494
South Asian	Sub	162	C=0.951	T=0.049
Other	Sub	3246	C=0.9606	T=0.0394

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=0.931966	T=0.068034
gnomAD - Genomes	Global	Study-wide	140192	C=0.938698	T=0.061302
gnomAD - Genomes	European	Sub	75956	C=0.97999	T=0.02001
gnomAD - Genomes	African	Sub	41982	C=0.86482	T=0.13518
gnomAD - Genomes	American	Sub	13650	C=0.94022	T=0.05978
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=0.9440	T=0.0560
gnomAD - Genomes	East Asian	Sub	3130	C=0.9211	T=0.0789
gnomAD - Genomes	Other	Sub	2152	C=0.9303	T=0.0697
Allele Frequency Aggregator	Total	Global	46658	C=0.96108	T=0.03892
Allele Frequency Aggregator	European	Sub	32398	C=0.97889	T=0.02111
Allele Frequency Aggregator	African	Sub	4938	C=0.8657	T=0.1343
Allele Frequency Aggregator	Latin American 2	Sub	4902	C=0.9506	T=0.0494
Allele Frequency Aggregator	Other	Sub	3246	C=0.9606	T=0.0394
Allele Frequency Aggregator	Latin American 1	Sub	574	C=0.929	T=0.071
Allele Frequency Aggregator	Asian	Sub	438	C=0.886	T=0.114
Allele Frequency Aggregator	South Asian	Sub	162	C=0.951	T=0.049
14KJPN	JAPANESE	Study-wide	28256	C=0.92384	T=0.07616
8.3KJPN	JAPANESE	Study-wide	16760	C=0.92584	T=0.07416
1000Genomes_30x	Global	Study-wide	6404	C=0.9155	T=0.0845
1000Genomes_30x	African	Sub	1786	C=0.8287	T=0.1713
1000Genomes_30x	Europe	Sub	1266	C=0.9739	T=0.0261
1000Genomes_30x	South Asian	Sub	1202	C=0.9626	T=0.0374
1000Genomes_30x	East Asian	Sub	1170	C=0.9111	T=0.0889
1000Genomes_30x	American	Sub	980	C=0.946	T=0.054
1000Genomes	Global	Study-wide	5008	C=0.9195	T=0.0805
1000Genomes	African	Sub	1322	C=0.8321	T=0.1679
1000Genomes	East Asian	Sub	1008	C=0.9117	T=0.0883
1000Genomes	Europe	Sub	1006	C=0.9722	T=0.0278
1000Genomes	South Asian	Sub	978	C=0.970	T=0.030
1000Genomes	American	Sub	694	C=0.950	T=0.050
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9821	T=0.0179
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9798	T=0.0202
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9833	T=0.0167
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9168	T=0.0832
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.977	T=0.023
Northern Sweden	ACPOP	Study-wide	600	C=0.960	T=0.040
HapMap	Global	Study-wide	326	C=0.914	T=0.086
HapMap	American	Sub	120	C=0.992	T=0.008
HapMap	African	Sub	118	C=0.839	T=0.161
HapMap	Asian	Sub	88	C=0.91	T=0.09
Qatari	Global	Study-wide	216	C=0.870	T=0.130
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.921	T=0.079
SGDP_PRJ	Global	Study-wide	84	C=0.37	T=0.63
The Danish reference pan genome	Danish	Study-wide	40	C=0.95	T=0.05
Siberian	Global	Study-wide	2	C=0.5	T=0.5

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.100354272C>T
GRCh37.p13 chr 1	NC_000001.10:g.100819828C>T
CDC14A RefSeqGene (LRG_1418)	NG_051602.2:g.14272C>T

Gene: CDC14A, cell division cycle 14A (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CDC14A transcript variant 4	NM_001319210.2:c.140+420C… NM_001319210.2:c.140+420C>T	N/A	Intron Variant
CDC14A transcript variant 5	NM_001319211.2:c.-35+420C… NM_001319211.2:c.-35+420C>T	N/A	Intron Variant
CDC14A transcript variant 6	NM_001319212.2:c.-652+420… NM_001319212.2:c.-652+420C>T	N/A	Intron Variant
CDC14A transcript variant 1	NM_003672.4:c.140+420C>T	N/A	Intron Variant
CDC14A transcript variant 2	NM_033312.3:c.140+420C>T	N/A	Intron Variant
CDC14A transcript variant 3	NM_033313.3:c.140+420C>T	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.100354272=	NC_000001.11:g.100354272C>T
GRCh37.p13 chr 1	NC_000001.10:g.100819828=	NC_000001.10:g.100819828C>T
CDC14A RefSeqGene (LRG_1418)	NG_051602.2:g.14272=	NG_051602.2:g.14272C>T
CDC14A transcript variant 4	NM_001319210.2:c.140+420=	NM_001319210.2:c.140+420C>T
CDC14A transcript variant 5	NM_001319211.2:c.-35+420=	NM_001319211.2:c.-35+420C>T
CDC14A transcript variant 6	NM_001319212.2:c.-652+420=	NM_001319212.2:c.-652+420C>T
CDC14A transcript variant 1	NM_003672.3:c.140+420=	NM_003672.3:c.140+420C>T
CDC14A transcript variant 1	NM_003672.4:c.140+420=	NM_003672.4:c.140+420C>T
CDC14A transcript variant 2	NM_033312.2:c.140+420=	NM_033312.2:c.140+420C>T
CDC14A transcript variant 2	NM_033312.3:c.140+420=	NM_033312.3:c.140+420C>T
CDC14A transcript variant 3	NM_033313.2:c.140+420=	NM_033313.2:c.140+420C>T
CDC14A transcript variant 3	NM_033313.3:c.140+420=	NM_033313.3:c.140+420C>T
CDC14A transcript variant X1	XM_005271294.1:c.143+420=	XM_005271294.1:c.143+420C>T
CDC14A transcript variant X2	XM_005271295.1:c.140+420=	XM_005271295.1:c.140+420C>T
CDC14A transcript variant X3	XM_005271296.1:c.143+420=	XM_005271296.1:c.143+420C>T
CDC14A transcript variant X4	XM_005271297.1:c.-35+420=	XM_005271297.1:c.-35+420C>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#.

55 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss11415421	Jul 11, 2003 (116)
2	SC_SNP	ss15394797	Feb 27, 2004 (120)
3	PERLEGEN	ss23162347	Sep 20, 2004 (123)
4	EGP_SNPS	ss35035693	May 24, 2005 (125)
5	BGI	ss102768241	Dec 01, 2009 (131)
6	ILLUMINA-UK	ss118922556	Feb 14, 2009 (130)
7	ILLUMINA	ss160887133	Dec 01, 2009 (131)
8	BUSHMAN	ss198838386	Jul 04, 2010 (132)
9	1000GENOMES	ss218551491	Jul 14, 2010 (132)
10	1000GENOMES	ss230658788	Jul 14, 2010 (132)
11	1000GENOMES	ss238325148	Jul 15, 2010 (132)
12	GMI	ss275946975	May 04, 2012 (137)
13	PJP	ss290581468	May 09, 2011 (134)
14	ILLUMINA	ss482590289	Sep 08, 2015 (146)
15	TISHKOFF	ss554485507	Apr 25, 2013 (138)
16	SSMP	ss648257311	Apr 25, 2013 (138)
17	EVA-GONL	ss975488814	Aug 21, 2014 (142)
18	JMKIDD_LAB	ss1068131301	Aug 21, 2014 (142)
19	1000GENOMES	ss1292127128	Aug 21, 2014 (142)
20	DDI	ss1425912566	Apr 01, 2015 (144)
21	EVA_GENOME_DK	ss1574274943	Apr 01, 2015 (144)
22	EVA_DECODE	ss1584866825	Apr 01, 2015 (144)
23	EVA_UK10K_ALSPAC	ss1600827743	Apr 01, 2015 (144)
24	EVA_UK10K_TWINSUK	ss1643821776	Apr 01, 2015 (144)
25	HAMMER_LAB	ss1794814805	Sep 08, 2015 (146)
26	WEILL_CORNELL_DGM	ss1918687779	Feb 12, 2016 (147)
27	JJLAB	ss2019865782	Sep 14, 2016 (149)
28	USC_VALOUEV	ss2147884286	Dec 20, 2016 (150)
29	HUMAN_LONGEVITY	ss2165073453	Dec 20, 2016 (150)
30	GRF	ss2697811486	Nov 08, 2017 (151)
31	GNOMAD	ss2758695352	Nov 08, 2017 (151)
32	SWEGEN	ss2987313902	Nov 08, 2017 (151)
33	CSHL	ss3343597987	Nov 08, 2017 (151)
34	ILLUMINA	ss3636017105	Oct 11, 2018 (152)
35	EGCUT_WGS	ss3655399579	Jul 12, 2019 (153)
36	EVA_DECODE	ss3687377339	Jul 12, 2019 (153)
37	ACPOP	ss3727318799	Jul 12, 2019 (153)
38	EVA	ss3746579831	Jul 12, 2019 (153)
39	KHV_HUMAN_GENOMES	ss3799580660	Jul 12, 2019 (153)
40	EVA	ss3826329411	Apr 25, 2020 (154)
41	SGDP_PRJ	ss3849487771	Apr 25, 2020 (154)
42	KRGDB	ss3894567033	Apr 25, 2020 (154)
43	TOPMED	ss4460878468	Apr 25, 2021 (155)
44	TOMMO_GENOMICS	ss5145336156	Apr 25, 2021 (155)
45	1000G_HIGH_COVERAGE	ss5243338745	Oct 12, 2022 (156)
46	EVA	ss5320704325	Oct 12, 2022 (156)
47	HUGCELL_USP	ss5444289967	Oct 12, 2022 (156)
48	1000G_HIGH_COVERAGE	ss5516189928	Oct 12, 2022 (156)
49	SANFORD_IMAGENETICS	ss5626141590	Oct 12, 2022 (156)
50	TOMMO_GENOMICS	ss5670502386	Oct 12, 2022 (156)
51	YY_MCH	ss5800863976	Oct 12, 2022 (156)
52	EVA	ss5832379064	Oct 12, 2022 (156)
53	EVA	ss5849035572	Oct 12, 2022 (156)
54	EVA	ss5909493369	Oct 12, 2022 (156)
55	EVA	ss5938003293	Oct 12, 2022 (156)
56	1000Genomes	NC_000001.10 - 100819828	Oct 11, 2018 (152)
57	1000Genomes_30x	NC_000001.11 - 100354272	Oct 12, 2022 (156)
58	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 100819828	Oct 11, 2018 (152)
59	Genetic variation in the Estonian population	NC_000001.10 - 100819828	Oct 11, 2018 (152)
60	The Danish reference pan genome	NC_000001.10 - 100819828	Apr 25, 2020 (154)
61	gnomAD - Genomes	NC_000001.11 - 100354272	Apr 25, 2021 (155)
62	Genome of the Netherlands Release 5	NC_000001.10 - 100819828	Apr 25, 2020 (154)
63	HapMap	NC_000001.11 - 100354272	Apr 25, 2020 (154)
64	KOREAN population from KRGDB	NC_000001.10 - 100819828	Apr 25, 2020 (154)
65	Northern Sweden	NC_000001.10 - 100819828	Jul 12, 2019 (153)
66	Qatari	NC_000001.10 - 100819828	Apr 25, 2020 (154)
67	SGDP_PRJ	NC_000001.10 - 100819828	Apr 25, 2020 (154)
68	Siberian	NC_000001.10 - 100819828	Apr 25, 2020 (154)
69	8.3KJPN	NC_000001.10 - 100819828	Apr 25, 2021 (155)
70	14KJPN	NC_000001.11 - 100354272	Oct 12, 2022 (156)
71	TopMed	NC_000001.11 - 100354272	Apr 25, 2021 (155)
72	UK 10K study - Twins	NC_000001.10 - 100819828	Oct 11, 2018 (152)
73	A Vietnamese Genetic Variation Database	NC_000001.10 - 100819828	Jul 12, 2019 (153)
74	ALFA	NC_000001.11 - 100354272	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
ss118922556, ss198838386, ss275946975, ss290581468, ss1584866825	NC_000001.9:100592415:C:T	NC_000001.11:100354271:C:T	(self)
2891556, 1595908, 1137827, 1630919, 692740, 1744427, 603664, 729709, 1504751, 400640, 3305463, 1595908, 343620, ss218551491, ss230658788, ss238325148, ss482590289, ss554485507, ss648257311, ss975488814, ss1068131301, ss1292127128, ss1425912566, ss1574274943, ss1600827743, ss1643821776, ss1794814805, ss1918687779, ss2019865782, ss2147884286, ss2697811486, ss2758695352, ss2987313902, ss3343597987, ss3636017105, ss3655399579, ss3727318799, ss3746579831, ss3826329411, ss3849487771, ss3894567033, ss5145336156, ss5320704325, ss5626141590, ss5832379064, ss5938003293	NC_000001.10:100819827:C:T	NC_000001.11:100354271:C:T	(self)
3715863, 20445037, 137695, 4339490, 24484803, 458765929, ss2165073453, ss3687377339, ss3799580660, ss4460878468, ss5243338745, ss5444289967, ss5516189928, ss5670502386, ss5800863976, ss5849035572, ss5909493369	NC_000001.11:100354271:C:T	NC_000001.11:100354271:C:T	(self)
ss11415421	NT_028050.12:1693498:C:T	NC_000001.11:100354271:C:T	(self)
ss15394797	NT_028050.13:9008771:C:T	NC_000001.11:100354271:C:T	(self)
ss23162347, ss35035693, ss102768241, ss160887133	NT_032977.9:70791745:C:T	NC_000001.11:100354271: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 rs7548466

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

rs7548466