Name: rs62239280
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.

rs62239280

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr22:17423309 (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>A / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.136711 (36186/264690, TOPMED)
T=0.147375 (20614/139874, GnomAD)
T=0.10110 (2857/28258, 14KJPN) (+ 16 more)
T=0.14343 (2665/18580, ALFA)
T=0.10012 (1678/16760, 8.3KJPN)
T=0.1357 (869/6404, 1000G_30x)
T=0.1386 (694/5008, 1000G)
T=0.1723 (772/4480, Estonian)
T=0.1578 (608/3854, ALSPAC)
T=0.1629 (604/3708, TWINSUK)
T=0.1144 (334/2920, KOREAN)
T=0.0993 (182/1832, Korea1K)
T=0.172 (172/998, GoNL)
T=0.173 (104/600, NorthernSweden)
T=0.079 (17/216, Qatari)
T=0.044 (9/206, Vietnamese)
C=0.485 (63/130, SGDP_PRJ)
T=0.15 (6/40, GENOME_DK)
C=0.42 (10/24, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CECR2 : 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	18580	C=0.85657	A=0.00000, T=0.14343
European	Sub	14130	C=0.84650	A=0.00000, T=0.15350
African	Sub	2794	C=0.8865	A=0.0000, T=0.1135
African Others	Sub	112	C=0.946	A=0.000, T=0.054
African American	Sub	2682	C=0.8840	A=0.0000, T=0.1160
Asian	Sub	112	C=0.920	A=0.000, T=0.080
East Asian	Sub	86	C=0.92	A=0.00, T=0.08
Other Asian	Sub	26	C=0.92	A=0.00, T=0.08
Latin American 1	Sub	146	C=0.870	A=0.000, T=0.130
Latin American 2	Sub	610	C=0.918	A=0.000, T=0.082
South Asian	Sub	98	C=0.86	A=0.00, T=0.14
Other	Sub	690	C=0.874	A=0.000, T=0.126

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").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	C=0.863289	T=0.136711
gnomAD - Genomes	Global	Study-wide	139874	C=0.852625	T=0.147375
gnomAD - Genomes	European	Sub	75792	C=0.83445	T=0.16555
gnomAD - Genomes	African	Sub	41870	C=0.86265	T=0.13735
gnomAD - Genomes	American	Sub	13618	C=0.89213	T=0.10787
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.9119	T=0.0881
gnomAD - Genomes	East Asian	Sub	3124	C=0.9145	T=0.0855
gnomAD - Genomes	Other	Sub	2146	C=0.8663	T=0.1337
14KJPN	JAPANESE	Study-wide	28258	C=0.89890	T=0.10110
Allele Frequency Aggregator	Total	Global	18580	C=0.85657	A=0.00000, T=0.14343
Allele Frequency Aggregator	European	Sub	14130	C=0.84650	A=0.00000, T=0.15350
Allele Frequency Aggregator	African	Sub	2794	C=0.8865	A=0.0000, T=0.1135
Allele Frequency Aggregator	Other	Sub	690	C=0.874	A=0.000, T=0.126
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.918	A=0.000, T=0.082
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.870	A=0.000, T=0.130
Allele Frequency Aggregator	Asian	Sub	112	C=0.920	A=0.000, T=0.080
Allele Frequency Aggregator	South Asian	Sub	98	C=0.86	A=0.00, T=0.14
8.3KJPN	JAPANESE	Study-wide	16760	C=0.89988	T=0.10012
1000Genomes_30x	Global	Study-wide	6404	C=0.8643	T=0.1357
1000Genomes_30x	African	Sub	1786	C=0.8718	T=0.1282
1000Genomes_30x	Europe	Sub	1266	C=0.8318	T=0.1682
1000Genomes_30x	South Asian	Sub	1202	C=0.7953	T=0.2047
1000Genomes_30x	East Asian	Sub	1170	C=0.9325	T=0.0675
1000Genomes_30x	American	Sub	980	C=0.896	T=0.104
1000Genomes	Global	Study-wide	5008	C=0.8614	T=0.1386
1000Genomes	African	Sub	1322	C=0.8722	T=0.1278
1000Genomes	East Asian	Sub	1008	C=0.9296	T=0.0704
1000Genomes	Europe	Sub	1006	C=0.8310	T=0.1690
1000Genomes	South Asian	Sub	978	C=0.783	T=0.217
1000Genomes	American	Sub	694	C=0.896	T=0.104
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.8277	T=0.1723
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.8422	T=0.1578
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.8371	T=0.1629
KOREAN population from KRGDB	KOREAN	Study-wide	2920	C=0.8856	T=0.1144
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9007	T=0.0993
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.828	T=0.172
Northern Sweden	ACPOP	Study-wide	600	C=0.827	T=0.173
Qatari	Global	Study-wide	216	C=0.921	T=0.079
A Vietnamese Genetic Variation Database	Global	Study-wide	206	C=0.956	T=0.044
SGDP_PRJ	Global	Study-wide	130	C=0.485	T=0.515
The Danish reference pan genome	Danish	Study-wide	40	C=0.85	T=0.15
Siberian	Global	Study-wide	24	C=0.42	T=0.58

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 22	NC_000022.11:g.17423309C>A
GRCh38.p14 chr 22	NC_000022.11:g.17423309C>T
GRCh37.p13 chr 22	NC_000022.10:g.17902357C>A
GRCh37.p13 chr 22	NC_000022.10:g.17902357C>T
CECR2 RefSeqGene	NG_033989.1:g.68361C>A
CECR2 RefSeqGene	NG_033989.1:g.68361C>T

Gene: CECR2, CECR2 histone acetyl-lysine reader (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CECR2 transcript variant 2	NM_001290046.2:c.-363-542… NM_001290046.2:c.-363-54279C>A	N/A	Intron Variant
CECR2 transcript variant 1	NM_001290047.2:c.126+5340… NM_001290047.2:c.126+53400C>A	N/A	Intron Variant
CECR2 transcript variant X2	XM_011546128.3:c.126+5340… XM_011546128.3:c.126+53400C>A	N/A	Intron Variant
CECR2 transcript variant X3	XM_011546129.3:c.126+5340… XM_011546129.3:c.126+53400C>A	N/A	Intron Variant
CECR2 transcript variant X5	XM_011546132.3:c.126+5340… XM_011546132.3:c.126+53400C>A	N/A	Intron Variant
CECR2 transcript variant X1	XM_017028785.2:c.126+5340… XM_017028785.2:c.126+53400C>A	N/A	Intron Variant
CECR2 transcript variant X6	XM_047441341.1:c.126+5340… XM_047441341.1:c.126+53400C>A	N/A	Intron Variant
CECR2 transcript variant X7	XM_047441342.1:c.126+5340… XM_047441342.1:c.126+53400C>A	N/A	Intron Variant
CECR2 transcript variant X8	XM_047441343.1:c.126+5340… XM_047441343.1:c.126+53400C>A	N/A	Intron Variant
CECR2 transcript variant X11	XM_047441345.1:c.126+5340… XM_047441345.1:c.126+53400C>A	N/A	Intron Variant
CECR2 transcript variant X10	XM_006724079.4:c.	N/A	Genic Upstream Transcript Variant
CECR2 transcript variant X4	XM_024452234.2:c.	N/A	Genic Upstream Transcript Variant
CECR2 transcript variant X9	XM_047441344.1:c.	N/A	Genic Upstream 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	C=	A	T
GRCh38.p14 chr 22	NC_000022.11:g.17423309=	NC_000022.11:g.17423309C>A	NC_000022.11:g.17423309C>T
GRCh37.p13 chr 22	NC_000022.10:g.17902357=	NC_000022.10:g.17902357C>A	NC_000022.10:g.17902357C>T
CECR2 RefSeqGene	NG_033989.1:g.68361=	NG_033989.1:g.68361C>A	NG_033989.1:g.68361C>T
CECR2 transcript variant 2	NM_001290046.2:c.-363-54279=	NM_001290046.2:c.-363-54279C>A	NM_001290046.2:c.-363-54279C>T
CECR2 transcript variant 1	NM_001290047.2:c.126+53400=	NM_001290047.2:c.126+53400C>A	NM_001290047.2:c.126+53400C>T
CECR2 transcript variant X2	XM_011546128.3:c.126+53400=	XM_011546128.3:c.126+53400C>A	XM_011546128.3:c.126+53400C>T
CECR2 transcript variant X3	XM_011546129.3:c.126+53400=	XM_011546129.3:c.126+53400C>A	XM_011546129.3:c.126+53400C>T
CECR2 transcript variant X5	XM_011546132.3:c.126+53400=	XM_011546132.3:c.126+53400C>A	XM_011546132.3:c.126+53400C>T
CECR2 transcript variant X1	XM_017028785.2:c.126+53400=	XM_017028785.2:c.126+53400C>A	XM_017028785.2:c.126+53400C>T
CECR2 transcript variant X6	XM_047441341.1:c.126+53400=	XM_047441341.1:c.126+53400C>A	XM_047441341.1:c.126+53400C>T
CECR2 transcript variant X7	XM_047441342.1:c.126+53400=	XM_047441342.1:c.126+53400C>A	XM_047441342.1:c.126+53400C>T
CECR2 transcript variant X8	XM_047441343.1:c.126+53400=	XM_047441343.1:c.126+53400C>A	XM_047441343.1:c.126+53400C>T
CECR2 transcript variant X11	XM_047441345.1:c.126+53400=	XM_047441345.1:c.126+53400C>A	XM_047441345.1:c.126+53400C>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#.

52 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCMHGSC_JDW	ss91871731	Mar 24, 2008 (129)
2	1000GENOMES	ss112539875	Jan 25, 2009 (130)
3	ENSEMBL	ss138332802	Dec 01, 2009 (131)
4	GMI	ss157013401	Dec 01, 2009 (131)
5	1000GENOMES	ss228610542	Jul 14, 2010 (132)
6	1000GENOMES	ss238016584	Jul 15, 2010 (132)
7	1000GENOMES	ss244147149	Jul 15, 2010 (132)
8	GMI	ss283580449	May 04, 2012 (137)
9	TISHKOFF	ss566550376	Apr 25, 2013 (138)
10	SSMP	ss662471680	Apr 25, 2013 (138)
11	EVA-GONL	ss995206271	Aug 21, 2014 (142)
12	JMKIDD_LAB	ss1082559409	Aug 21, 2014 (142)
13	1000GENOMES	ss1366622175	Aug 21, 2014 (142)
14	EVA_GENOME_DK	ss1579697786	Apr 01, 2015 (144)
15	EVA_UK10K_ALSPAC	ss1639725051	Apr 01, 2015 (144)
16	EVA_UK10K_TWINSUK	ss1682719084	Apr 01, 2015 (144)
17	EVA_DECODE	ss1699275778	Apr 01, 2015 (144)
18	HAMMER_LAB	ss1809726668	Sep 08, 2015 (146)
19	WEILL_CORNELL_DGM	ss1938765459	Feb 12, 2016 (147)
20	GENOMED	ss1969243780	Jul 19, 2016 (147)
21	JJLAB	ss2030156026	Sep 14, 2016 (149)
22	USC_VALOUEV	ss2158764873	Dec 20, 2016 (150)
23	HUMAN_LONGEVITY	ss2246347006	Dec 20, 2016 (150)
24	GRF	ss2704505215	Nov 08, 2017 (151)
25	GNOMAD	ss2972797006	Nov 08, 2017 (151)
26	SWEGEN	ss3019053700	Nov 08, 2017 (151)
27	BIOINF_KMB_FNS_UNIBA	ss3028916266	Nov 08, 2017 (151)
28	CSHL	ss3352767118	Nov 08, 2017 (151)
29	EGCUT_WGS	ss3685595363	Jul 13, 2019 (153)
30	EVA_DECODE	ss3707922788	Jul 13, 2019 (153)
31	ACPOP	ss3743808463	Jul 13, 2019 (153)
32	EVA	ss3759211401	Jul 13, 2019 (153)
33	KHV_HUMAN_GENOMES	ss3822378607	Jul 13, 2019 (153)
34	EVA	ss3835919316	Apr 27, 2020 (154)
35	EVA	ss3841588451	Apr 27, 2020 (154)
36	EVA	ss3847103244	Apr 27, 2020 (154)
37	SGDP_PRJ	ss3890215317	Apr 27, 2020 (154)
38	KRGDB	ss3940592198	Apr 27, 2020 (154)
39	KOGIC	ss3983350339	Apr 27, 2020 (154)
40	TOPMED	ss5104615870	Apr 27, 2021 (155)
41	TOMMO_GENOMICS	ss5231958549	Apr 27, 2021 (155)
42	1000G_HIGH_COVERAGE	ss5310602165	Oct 16, 2022 (156)
43	EVA	ss5440426754	Oct 16, 2022 (156)
44	HUGCELL_USP	ss5502522626	Oct 16, 2022 (156)
45	1000G_HIGH_COVERAGE	ss5617933652	Oct 16, 2022 (156)
46	SANFORD_IMAGENETICS	ss5664199781	Oct 16, 2022 (156)
47	TOMMO_GENOMICS	ss5792877208	Oct 16, 2022 (156)
48	YY_MCH	ss5818579477	Oct 16, 2022 (156)
49	EVA	ss5821877359	Oct 16, 2022 (156)
50	EVA	ss5853340049	Oct 16, 2022 (156)
51	EVA	ss5881291651	Oct 16, 2022 (156)
52	EVA	ss5959077644	Oct 16, 2022 (156)
53	1000Genomes	NC_000022.10 - 17902357	Oct 12, 2018 (152)
54	1000Genomes_30x	NC_000022.11 - 17423309	Oct 16, 2022 (156)
55	The Avon Longitudinal Study of Parents and Children	NC_000022.10 - 17902357	Oct 12, 2018 (152)
56	Genetic variation in the Estonian population	NC_000022.10 - 17902357	Oct 12, 2018 (152)
57	The Danish reference pan genome	NC_000022.10 - 17902357	Apr 27, 2020 (154)
58	gnomAD - Genomes	NC_000022.11 - 17423309	Apr 27, 2021 (155)
59	Genome of the Netherlands Release 5	NC_000022.10 - 17902357	Apr 27, 2020 (154)
60	KOREAN population from KRGDB	NC_000022.10 - 17902357	Apr 27, 2020 (154)
61	Korean Genome Project	NC_000022.11 - 17423309	Apr 27, 2020 (154)
62	Northern Sweden	NC_000022.10 - 17902357	Jul 13, 2019 (153)
63	Qatari	NC_000022.10 - 17902357	Apr 27, 2020 (154)
64	SGDP_PRJ	NC_000022.10 - 17902357	Apr 27, 2020 (154)
65	Siberian	NC_000022.10 - 17902357	Apr 27, 2020 (154)
66	8.3KJPN	NC_000022.10 - 17902357	Apr 27, 2021 (155)
67	14KJPN	NC_000022.11 - 17423309	Oct 16, 2022 (156)
68	TopMed	NC_000022.11 - 17423309	Apr 27, 2021 (155)
69	UK 10K study - Twins	NC_000022.10 - 17902357	Oct 12, 2018 (152)
70	A Vietnamese Genetic Variation Database	NC_000022.10 - 17902357	Jul 13, 2019 (153)
71	ALFA	NC_000022.11 - 17423309	Apr 27, 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
7900588026	NC_000022.11:17423308:C:A	NC_000022.11:17423308:C:A	(self)
ss91871731, ss112539875, ss283580449, ss1699275778	NC_000022.9:16282356:C:T	NC_000022.11:17423308:C:T	(self)
80154330, 44349992, 31333611, 5862725, 19758580, 47769592, 17093328, 20807381, 42232297, 11281227, 89927856, 44349992, 9785264, ss228610542, ss238016584, ss244147149, ss566550376, ss662471680, ss995206271, ss1082559409, ss1366622175, ss1579697786, ss1639725051, ss1682719084, ss1809726668, ss1938765459, ss1969243780, ss2030156026, ss2158764873, ss2704505215, ss2972797006, ss3019053700, ss3352767118, ss3685595363, ss3743808463, ss3759211401, ss3835919316, ss3841588451, ss3890215317, ss3940592198, ss5231958549, ss5440426754, ss5664199781, ss5821877359, ss5959077644	NC_000022.10:17902356:C:T	NC_000022.11:17423308:C:T	(self)
105459587, 566093357, 39728340, 126714312, 379724817, 7900588026, ss2246347006, ss3028916266, ss3707922788, ss3822378607, ss3847103244, ss3983350339, ss5104615870, ss5310602165, ss5502522626, ss5617933652, ss5792877208, ss5818579477, ss5853340049, ss5881291651	NC_000022.11:17423308:C:T	NC_000022.11:17423308:C:T	(self)
ss138332802, ss157013401	NT_011519.10:1054506:C:T	NC_000022.11:17423308: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 rs62239280

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

rs62239280