Name: rs730002
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.

rs730002

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:169552682 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.012248 (3242/264690, TOPMED)
C=0.011874 (1666/140312, GnomAD)
C=0.00815 (140/17174, ALFA) (+ 8 more)
C=0.0139 (89/6404, 1000G_30x)
C=0.0138 (69/5008, 1000G)
C=0.0003 (1/3854, ALSPAC)
C=0.0000 (0/3708, TWINSUK)
C=0.020 (20/998, HapMap)
C=0.002 (1/626, Chileans)
T=0.5 (3/6, SGDP_PRJ)
C=0.5 (3/6, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: WDR27 : 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	17174	T=0.99185	C=0.00815
European	Sub	11202	T=0.99991	C=0.00009
African	Sub	3618	T=0.9643	C=0.0357
African Others	Sub	126	T=0.960	C=0.040
African American	Sub	3492	T=0.9645	C=0.0355
Asian	Sub	160	T=1.000	C=0.000
East Asian	Sub	102	T=1.000	C=0.000
Other Asian	Sub	58	T=1.00	C=0.00
Latin American 1	Sub	212	T=0.995	C=0.005
Latin American 2	Sub	752	T=0.996	C=0.004
South Asian	Sub	110	T=1.000	C=0.000
Other	Sub	1120	T=0.9946	C=0.0054

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=0.987752	C=0.012248
gnomAD - Genomes	Global	Study-wide	140312	T=0.988126	C=0.011874
gnomAD - Genomes	European	Sub	75978	T=0.99995	C=0.00005
gnomAD - Genomes	African	Sub	42058	T=0.96203	C=0.03797
gnomAD - Genomes	American	Sub	13664	T=0.99663	C=0.00337
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=1.0000	C=0.0000
gnomAD - Genomes	East Asian	Sub	3134	T=1.0000	C=0.0000
gnomAD - Genomes	Other	Sub	2154	T=0.9912	C=0.0088
Allele Frequency Aggregator	Total	Global	17174	T=0.99185	C=0.00815
Allele Frequency Aggregator	European	Sub	11202	T=0.99991	C=0.00009
Allele Frequency Aggregator	African	Sub	3618	T=0.9643	C=0.0357
Allele Frequency Aggregator	Other	Sub	1120	T=0.9946	C=0.0054
Allele Frequency Aggregator	Latin American 2	Sub	752	T=0.996	C=0.004
Allele Frequency Aggregator	Latin American 1	Sub	212	T=0.995	C=0.005
Allele Frequency Aggregator	Asian	Sub	160	T=1.000	C=0.000
Allele Frequency Aggregator	South Asian	Sub	110	T=1.000	C=0.000
1000Genomes_30x	Global	Study-wide	6404	T=0.9861	C=0.0139
1000Genomes_30x	African	Sub	1786	T=0.9524	C=0.0476
1000Genomes_30x	Europe	Sub	1266	T=1.0000	C=0.0000
1000Genomes_30x	South Asian	Sub	1202	T=1.0000	C=0.0000
1000Genomes_30x	East Asian	Sub	1170	T=1.0000	C=0.0000
1000Genomes_30x	American	Sub	980	T=0.996	C=0.004
1000Genomes	Global	Study-wide	5008	T=0.9862	C=0.0138
1000Genomes	African	Sub	1322	T=0.9493	C=0.0507
1000Genomes	East Asian	Sub	1008	T=1.0000	C=0.0000
1000Genomes	Europe	Sub	1006	T=1.0000	C=0.0000
1000Genomes	South Asian	Sub	978	T=1.000	C=0.000
1000Genomes	American	Sub	694	T=0.997	C=0.003
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9997	C=0.0003
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=1.0000	C=0.0000
HapMap	Global	Study-wide	998	T=0.980	C=0.020
HapMap	African	Sub	690	T=0.978	C=0.022
HapMap	American	Sub	218	T=0.977	C=0.023
HapMap	Asian	Sub	90	T=1.00	C=0.00
Chileans	Chilean	Study-wide	626	T=0.998	C=0.002
SGDP_PRJ	Global	Study-wide	6	T=0.5	C=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 6	NC_000006.12:g.169552682T>C
GRCh37.p13 chr 6	NC_000006.11:g.169952778T>C
WDR27 RefSeqGene (LRG_1071)	NG_046155.1:g.154382A>G

Gene: WDR27, WD repeat domain 27 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
WDR27 transcript variant 2	NM_001202550.2:c.2142+301… NM_001202550.2:c.2142+30154A>G	N/A	Intron Variant
WDR27 transcript variant 3	NM_001350623.2:c.1950+301… NM_001350623.2:c.1950+30154A>G	N/A	Intron Variant
WDR27 transcript variant 1	NM_182552.5:c.2645+19737A… NM_182552.5:c.2645+19737A>G	N/A	Intron Variant
WDR27 transcript variant 4	NM_001350624.2:c.	N/A	Genic Downstream Transcript Variant
WDR27 transcript variant 5	NM_001350625.2:c.	N/A	Genic Downstream Transcript Variant
WDR27 transcript variant 6	NR_146875.2:n.	N/A	Intron Variant
WDR27 transcript variant 7	NR_146876.2:n.	N/A	Genic Downstream Transcript Variant
WDR27 transcript variant X5	XM_011535685.4:c.2524-122… XM_011535685.4:c.2524-1221A>G	N/A	Intron Variant
WDR27 transcript variant X7	XM_011535687.4:c.2523+301… XM_011535687.4:c.2523+30154A>G	N/A	Intron Variant
WDR27 transcript variant X8	XM_011535688.4:c.2523+301… XM_011535688.4:c.2523+30154A>G	N/A	Intron Variant
WDR27 transcript variant X10	XM_011535691.4:c.2523+301… XM_011535691.4:c.2523+30154A>G	N/A	Intron Variant
WDR27 transcript variant X11	XM_011535692.4:c.2523+301… XM_011535692.4:c.2523+30154A>G	N/A	Intron Variant
WDR27 transcript variant X6	XM_017010660.3:c.2523+301… XM_017010660.3:c.2523+30154A>G	N/A	Intron Variant
WDR27 transcript variant X15	XM_017010669.2:c.1950+301… XM_017010669.2:c.1950+30154A>G	N/A	Intron Variant
WDR27 transcript variant X4	XM_047418584.1:c.2523+301… XM_047418584.1:c.2523+30154A>G	N/A	Intron Variant
WDR27 transcript variant X1	XM_011535682.4:c.	N/A	Genic Downstream Transcript Variant
WDR27 transcript variant X3	XM_011535684.4:c.	N/A	Genic Downstream Transcript Variant
WDR27 transcript variant X12	XM_011535693.4:c.	N/A	Genic Downstream Transcript Variant
WDR27 transcript variant X22	XM_011535697.4:c.	N/A	Genic Downstream Transcript Variant
WDR27 transcript variant X17	XM_017010672.3:c.	N/A	Genic Downstream Transcript Variant
WDR27 transcript variant X13	XM_047418585.1:c.	N/A	Genic Downstream Transcript Variant
WDR27 transcript variant X14	XM_047418586.1:c.	N/A	Genic Downstream Transcript Variant
WDR27 transcript variant X16	XM_047418587.1:c.	N/A	Genic Downstream Transcript Variant
WDR27 transcript variant X19	XM_047418588.1:c.	N/A	Genic Downstream Transcript Variant
WDR27 transcript variant X20	XM_047418589.1:c.	N/A	Genic Downstream Transcript Variant
WDR27 transcript variant X21	XM_047418590.1:c.	N/A	Genic Downstream Transcript Variant
WDR27 transcript variant X9	XR_007059231.1:n.	N/A	Intron Variant
WDR27 transcript variant X2	XR_007059230.1:n.	N/A	Genic Downstream Transcript Variant
WDR27 transcript variant X18	XR_007059233.1:n.	N/A	Genic Downstream Transcript 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=	C
GRCh38.p14 chr 6	NC_000006.12:g.169552682=	NC_000006.12:g.169552682T>C
GRCh37.p13 chr 6	NC_000006.11:g.169952778=	NC_000006.11:g.169952778T>C
WDR27 RefSeqGene (LRG_1071)	NG_046155.1:g.154382=	NG_046155.1:g.154382A>G
WDR27 transcript variant 2	NM_001202550.1:c.2142+30154=	NM_001202550.1:c.2142+30154A>G
WDR27 transcript variant 2	NM_001202550.2:c.2142+30154=	NM_001202550.2:c.2142+30154A>G
WDR27 transcript variant 3	NM_001350623.2:c.1950+30154=	NM_001350623.2:c.1950+30154A>G
WDR27 transcript variant 1	NM_182552.4:c.2645+19737=	NM_182552.4:c.2645+19737A>G
WDR27 transcript variant 1	NM_182552.5:c.2645+19737=	NM_182552.5:c.2645+19737A>G
WDR27 transcript variant X1	XM_005266894.1:c.1722+30154=	XM_005266894.1:c.1722+30154A>G
WDR27 transcript variant X2	XM_005266895.1:c.1722+30154=	XM_005266895.1:c.1722+30154A>G
WDR27 transcript variant X5	XM_011535685.4:c.2524-1221=	XM_011535685.4:c.2524-1221A>G
WDR27 transcript variant X7	XM_011535687.4:c.2523+30154=	XM_011535687.4:c.2523+30154A>G
WDR27 transcript variant X8	XM_011535688.4:c.2523+30154=	XM_011535688.4:c.2523+30154A>G
WDR27 transcript variant X10	XM_011535691.4:c.2523+30154=	XM_011535691.4:c.2523+30154A>G
WDR27 transcript variant X11	XM_011535692.4:c.2523+30154=	XM_011535692.4:c.2523+30154A>G
WDR27 transcript variant X6	XM_017010660.3:c.2523+30154=	XM_017010660.3:c.2523+30154A>G
WDR27 transcript variant X15	XM_017010669.2:c.1950+30154=	XM_017010669.2:c.1950+30154A>G
WDR27 transcript variant X4	XM_047418584.1:c.2523+30154=	XM_047418584.1:c.2523+30154A>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#.

21 SubSNP, 10 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss74922	Oct 05, 2000 (86)
2	AFFY	ss66274526	Jul 04, 2010 (132)
3	AFFY	ss75924921	Dec 07, 2007 (129)
4	KRIBB_YJKIM	ss81434984	Dec 15, 2007 (130)
5	1000GENOMES	ss222840391	Jul 14, 2010 (132)
6	1000GENOMES	ss1323435242	Aug 21, 2014 (142)
7	EVA_UK10K_ALSPAC	ss1617323946	Apr 01, 2015 (144)
8	EVA_UK10K_TWINSUK	ss1660317979	Apr 01, 2015 (144)
9	HUMAN_LONGEVITY	ss2290778837	Dec 20, 2016 (150)
10	GNOMAD	ss2848373931	Nov 08, 2017 (151)
11	EVA_DECODE	ss3718853362	Jul 13, 2019 (153)
12	SGDP_PRJ	ss3866340014	Apr 26, 2020 (154)
13	TOPMED	ss4731578882	Apr 26, 2021 (155)
14	1000G_HIGH_COVERAGE	ss5271376496	Oct 14, 2022 (156)
15	EVA	ss5370873598	Oct 14, 2022 (156)
16	HUGCELL_USP	ss5468721948	Oct 14, 2022 (156)
17	1000G_HIGH_COVERAGE	ss5558816652	Oct 14, 2022 (156)
18	SANFORD_IMAGENETICS	ss5642083753	Oct 14, 2022 (156)
19	EVA	ss5887132900	Oct 14, 2022 (156)
20	EVA	ss5971266033	Oct 14, 2022 (156)
21	EVA	ss5971266034	Oct 14, 2022 (156)
22	1000Genomes	NC_000006.11 - 169952778	Oct 12, 2018 (152)
23	1000Genomes_30x	NC_000006.12 - 169552682	Oct 14, 2022 (156)
24	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 169952778	Oct 12, 2018 (152)
25	Chileans	NC_000006.11 - 169952778	Apr 26, 2020 (154)
26	gnomAD - Genomes	NC_000006.12 - 169552682	Apr 26, 2021 (155)
27	HapMap	NC_000006.12 - 169552682	Apr 26, 2020 (154)
28	SGDP_PRJ	NC_000006.11 - 169952778	Apr 26, 2020 (154)
29	TopMed	NC_000006.12 - 169552682	Apr 26, 2021 (155)
30	UK 10K study - Twins	NC_000006.11 - 169952778	Oct 12, 2018 (152)
31	ALFA	NC_000006.12 - 169552682	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)
rs58547695	Feb 26, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
35348029, 19717466, 398865, 18356994, 19717466, ss222840391, ss1323435242, ss1617323946, ss1660317979, ss2848373931, ss3866340014, ss5370873598, ss5642083753, ss5971266033, ss5971266034	NC_000006.11:169952777:T:C	NC_000006.12:169552681:T:C	(self)
46342587, 249395311, 3314392, 568956440, 6472285992, ss2290778837, ss3718853362, ss4731578882, ss5271376496, ss5468721948, ss5558816652, ss5887132900	NC_000006.12:169552681:T:C	NC_000006.12:169552681:T:C	(self)
ss74922, ss75924921, ss81434984	NT_025741.15:74122234:T:C	NC_000006.12:169552681:T:C	(self)
ss66274526	NT_025741.16:109322747:T:C	NC_000006.12:169552681:T: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 rs730002

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

rs730002