Name: rs73153492
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.

rs73153492

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr22:17390451 (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>A / T>C / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.134081 (35490/264690, TOPMED)
C=0.25232 (7130/28258, 14KJPN)
C=0.09279 (2620/28236, ALFA) (+ 14 more)
C=0.25430 (4262/16760, 8.3KJPN)
C=0.1458 (934/6404, 1000G_30x)
C=0.1460 (731/5008, 1000G)
C=0.1344 (602/4480, Estonian)
C=0.1245 (480/3854, ALSPAC)
C=0.1284 (476/3708, TWINSUK)
C=0.2512 (734/2922, KOREAN)
C=0.155 (155/998, GoNL)
C=0.175 (105/600, NorthernSweden)
C=0.185 (40/216, Qatari)
C=0.123 (26/212, Vietnamese)
T=0.456 (72/158, SGDP_PRJ)
C=0.07 (3/40, GENOME_DK)
T=0.45 (10/22, 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	28236	T=0.90721	A=0.00000, C=0.09279
European	Sub	23038	T=0.89882	A=0.00000, C=0.10118
African	Sub	2640	T=0.9523	A=0.0000, C=0.0477
African Others	Sub	106	T=0.972	A=0.000, C=0.028
African American	Sub	2534	T=0.9515	A=0.0000, C=0.0485
Asian	Sub	82	T=0.96	A=0.00, C=0.04
East Asian	Sub	60	T=0.95	A=0.00, C=0.05
Other Asian	Sub	22	T=1.00	A=0.00, C=0.00
Latin American 1	Sub	138	T=0.971	A=0.000, C=0.029
Latin American 2	Sub	530	T=0.972	A=0.000, C=0.028
South Asian	Sub	98	T=0.98	A=0.00, C=0.02
Other	Sub	1710	T=0.9187	A=0.0000, C=0.0813

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	T=0.865919	C=0.134081
14KJPN	JAPANESE	Study-wide	28258	T=0.74768	C=0.25232
Allele Frequency Aggregator	Total	Global	28236	T=0.90721	A=0.00000, C=0.09279
Allele Frequency Aggregator	European	Sub	23038	T=0.89882	A=0.00000, C=0.10118
Allele Frequency Aggregator	African	Sub	2640	T=0.9523	A=0.0000, C=0.0477
Allele Frequency Aggregator	Other	Sub	1710	T=0.9187	A=0.0000, C=0.0813
Allele Frequency Aggregator	Latin American 2	Sub	530	T=0.972	A=0.000, C=0.028
Allele Frequency Aggregator	Latin American 1	Sub	138	T=0.971	A=0.000, C=0.029
Allele Frequency Aggregator	South Asian	Sub	98	T=0.98	A=0.00, C=0.02
Allele Frequency Aggregator	Asian	Sub	82	T=0.96	A=0.00, C=0.04
8.3KJPN	JAPANESE	Study-wide	16760	T=0.74570	C=0.25430
1000Genomes_30x	Global	Study-wide	6404	T=0.8542	C=0.1458
1000Genomes_30x	African	Sub	1786	T=0.8611	C=0.1389
1000Genomes_30x	Europe	Sub	1266	T=0.8610	C=0.1390
1000Genomes_30x	South Asian	Sub	1202	T=0.9068	C=0.0932
1000Genomes_30x	East Asian	Sub	1170	T=0.7752	C=0.2248
1000Genomes_30x	American	Sub	980	T=0.862	C=0.138
1000Genomes	Global	Study-wide	5008	T=0.8540	C=0.1460
1000Genomes	African	Sub	1322	T=0.8563	C=0.1437
1000Genomes	East Asian	Sub	1008	T=0.7778	C=0.2222
1000Genomes	Europe	Sub	1006	T=0.8628	C=0.1372
1000Genomes	South Asian	Sub	978	T=0.911	C=0.089
1000Genomes	American	Sub	694	T=0.867	C=0.133
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.8656	C=0.1344
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.8755	C=0.1245
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.8716	C=0.1284
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.7488	C=0.2512
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.845	C=0.155
Northern Sweden	ACPOP	Study-wide	600	T=0.825	C=0.175
Qatari	Global	Study-wide	216	T=0.815	C=0.185
A Vietnamese Genetic Variation Database	Global	Study-wide	212	T=0.877	C=0.123
SGDP_PRJ	Global	Study-wide	158	T=0.456	C=0.544
The Danish reference pan genome	Danish	Study-wide	40	T=0.93	C=0.07
Siberian	Global	Study-wide	22	T=0.45	C=0.55

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.17390451T>A
GRCh38.p14 chr 22	NC_000022.11:g.17390451T>C
GRCh38.p14 chr 22	NC_000022.11:g.17390451T>G
GRCh37.p13 chr 22	NC_000022.10:g.17870340T>A
GRCh37.p13 chr 22	NC_000022.10:g.17870340T>C
GRCh37.p13 chr 22	NC_000022.10:g.17870340T>G
CECR2 RefSeqGene	NG_033989.1:g.35503T>A
CECR2 RefSeqGene	NG_033989.1:g.35503T>C
CECR2 RefSeqGene	NG_033989.1:g.35503T>G

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.-364+304… NM_001290046.2:c.-364+30428T>A	N/A	Intron Variant
CECR2 transcript variant 1	NM_001290047.2:c.126+2054… NM_001290047.2:c.126+20542T>A	N/A	Intron Variant
CECR2 transcript variant X2	XM_011546128.3:c.126+2054… XM_011546128.3:c.126+20542T>A	N/A	Intron Variant
CECR2 transcript variant X3	XM_011546129.3:c.126+2054… XM_011546129.3:c.126+20542T>A	N/A	Intron Variant
CECR2 transcript variant X5	XM_011546132.3:c.126+2054… XM_011546132.3:c.126+20542T>A	N/A	Intron Variant
CECR2 transcript variant X1	XM_017028785.2:c.126+2054… XM_017028785.2:c.126+20542T>A	N/A	Intron Variant
CECR2 transcript variant X6	XM_047441341.1:c.126+2054… XM_047441341.1:c.126+20542T>A	N/A	Intron Variant
CECR2 transcript variant X7	XM_047441342.1:c.126+2054… XM_047441342.1:c.126+20542T>A	N/A	Intron Variant
CECR2 transcript variant X8	XM_047441343.1:c.126+2054… XM_047441343.1:c.126+20542T>A	N/A	Intron Variant
CECR2 transcript variant X11	XM_047441345.1:c.126+2054… XM_047441345.1:c.126+20542T>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	T=	A	C	G
GRCh38.p14 chr 22	NC_000022.11:g.17390451=	NC_000022.11:g.17390451T>A	NC_000022.11:g.17390451T>C	NC_000022.11:g.17390451T>G
GRCh37.p13 chr 22	NC_000022.10:g.17870340=	NC_000022.10:g.17870340T>A	NC_000022.10:g.17870340T>C	NC_000022.10:g.17870340T>G
CECR2 RefSeqGene	NG_033989.1:g.35503=	NG_033989.1:g.35503T>A	NG_033989.1:g.35503T>C	NG_033989.1:g.35503T>G
CECR2 transcript variant 2	NM_001290046.2:c.-364+30428=	NM_001290046.2:c.-364+30428T>A	NM_001290046.2:c.-364+30428T>C	NM_001290046.2:c.-364+30428T>G
CECR2 transcript variant 1	NM_001290047.2:c.126+20542=	NM_001290047.2:c.126+20542T>A	NM_001290047.2:c.126+20542T>C	NM_001290047.2:c.126+20542T>G
CECR2 transcript variant X2	XM_011546128.3:c.126+20542=	XM_011546128.3:c.126+20542T>A	XM_011546128.3:c.126+20542T>C	XM_011546128.3:c.126+20542T>G
CECR2 transcript variant X3	XM_011546129.3:c.126+20542=	XM_011546129.3:c.126+20542T>A	XM_011546129.3:c.126+20542T>C	XM_011546129.3:c.126+20542T>G
CECR2 transcript variant X5	XM_011546132.3:c.126+20542=	XM_011546132.3:c.126+20542T>A	XM_011546132.3:c.126+20542T>C	XM_011546132.3:c.126+20542T>G
CECR2 transcript variant X1	XM_017028785.2:c.126+20542=	XM_017028785.2:c.126+20542T>A	XM_017028785.2:c.126+20542T>C	XM_017028785.2:c.126+20542T>G
CECR2 transcript variant X6	XM_047441341.1:c.126+20542=	XM_047441341.1:c.126+20542T>A	XM_047441341.1:c.126+20542T>C	XM_047441341.1:c.126+20542T>G
CECR2 transcript variant X7	XM_047441342.1:c.126+20542=	XM_047441342.1:c.126+20542T>A	XM_047441342.1:c.126+20542T>C	XM_047441342.1:c.126+20542T>G
CECR2 transcript variant X8	XM_047441343.1:c.126+20542=	XM_047441343.1:c.126+20542T>A	XM_047441343.1:c.126+20542T>C	XM_047441343.1:c.126+20542T>G
CECR2 transcript variant X11	XM_047441345.1:c.126+20542=	XM_047441345.1:c.126+20542T>A	XM_047441345.1:c.126+20542T>C	XM_047441345.1:c.126+20542T>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#.

60 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss112539637	Feb 14, 2009 (130)
2	GMI	ss157012893	Dec 01, 2009 (131)
3	1000GENOMES	ss228610382	Jul 14, 2010 (132)
4	1000GENOMES	ss238016481	Jul 15, 2010 (132)
5	1000GENOMES	ss244147059	Jul 15, 2010 (132)
6	GMI	ss283580288	May 04, 2012 (137)
7	ILLUMINA	ss482994376	May 04, 2012 (137)
8	ILLUMINA	ss484286421	May 04, 2012 (137)
9	ILLUMINA	ss534964076	Sep 08, 2015 (146)
10	TISHKOFF	ss566550185	Apr 25, 2013 (138)
11	SSMP	ss662471476	Apr 25, 2013 (138)
12	ILLUMINA	ss780115714	Sep 08, 2015 (146)
13	ILLUMINA	ss781946171	Sep 08, 2015 (146)
14	ILLUMINA	ss835598581	Sep 08, 2015 (146)
15	EVA-GONL	ss995205937	Aug 21, 2014 (142)
16	JMKIDD_LAB	ss1082559194	Aug 21, 2014 (142)
17	1000GENOMES	ss1366621033	Aug 21, 2014 (142)
18	DDI	ss1429214174	Apr 01, 2015 (144)
19	EVA_GENOME_DK	ss1579697673	Apr 01, 2015 (144)
20	EVA_UK10K_ALSPAC	ss1639724522	Apr 01, 2015 (144)
21	EVA_UK10K_TWINSUK	ss1682718555	Apr 01, 2015 (144)
22	EVA_DECODE	ss1699275417	Apr 01, 2015 (144)
23	HAMMER_LAB	ss1809726485	Sep 08, 2015 (146)
24	WEILL_CORNELL_DGM	ss1938765146	Feb 12, 2016 (147)
25	JJLAB	ss2030155852	Sep 14, 2016 (149)
26	USC_VALOUEV	ss2158764665	Dec 20, 2016 (150)
27	SYSTEMSBIOZJU	ss2629576178	Nov 08, 2017 (151)
28	ILLUMINA	ss2633860736	Nov 08, 2017 (151)
29	GRF	ss2704504948	Nov 08, 2017 (151)
30	GNOMAD	ss2972793762	Nov 08, 2017 (151)
31	SWEGEN	ss3019053126	Nov 08, 2017 (151)
32	BIOINF_KMB_FNS_UNIBA	ss3028916186	Nov 08, 2017 (151)
33	CSHL	ss3352766932	Nov 08, 2017 (151)
34	ILLUMINA	ss3628502195	Oct 12, 2018 (152)
35	ILLUMINA	ss3631813283	Oct 12, 2018 (152)
36	ILLUMINA	ss3642210337	Oct 12, 2018 (152)
37	EGCUT_WGS	ss3685594811	Jul 13, 2019 (153)
38	EVA_DECODE	ss3707922149	Jul 13, 2019 (153)
39	ACPOP	ss3743808151	Jul 13, 2019 (153)
40	EVA	ss3759211044	Jul 13, 2019 (153)
41	KHV_HUMAN_GENOMES	ss3822378190	Jul 13, 2019 (153)
42	EVA	ss3835919162	Apr 27, 2020 (154)
43	EVA	ss3841588365	Apr 27, 2020 (154)
44	EVA	ss3847103148	Apr 27, 2020 (154)
45	SGDP_PRJ	ss3890214658	Apr 27, 2020 (154)
46	KRGDB	ss3940591386	Apr 27, 2020 (154)
47	TOPMED	ss5104606717	Apr 27, 2021 (155)
48	TOMMO_GENOMICS	ss5231956989	Apr 27, 2021 (155)
49	1000G_HIGH_COVERAGE	ss5310601044	Oct 16, 2022 (156)
50	EVA	ss5316045593	Oct 16, 2022 (156)
51	EVA	ss5440425048	Oct 16, 2022 (156)
52	HUGCELL_USP	ss5502521677	Oct 16, 2022 (156)
53	1000G_HIGH_COVERAGE	ss5617932121	Oct 16, 2022 (156)
54	SANFORD_IMAGENETICS	ss5664199138	Oct 16, 2022 (156)
55	TOMMO_GENOMICS	ss5792875244	Oct 16, 2022 (156)
56	YY_MCH	ss5818579146	Oct 16, 2022 (156)
57	EVA	ss5821876936	Oct 16, 2022 (156)
58	EVA	ss5853339922	Oct 16, 2022 (156)
59	EVA	ss5881290482	Oct 16, 2022 (156)
60	EVA	ss5959077049	Oct 16, 2022 (156)
61	1000Genomes	NC_000022.10 - 17870340	Oct 12, 2018 (152)
62	1000Genomes_30x	NC_000022.11 - 17390451	Oct 16, 2022 (156)
63	The Avon Longitudinal Study of Parents and Children	NC_000022.10 - 17870340	Oct 12, 2018 (152)
64	Genetic variation in the Estonian population	NC_000022.10 - 17870340	Oct 12, 2018 (152)
65	The Danish reference pan genome	NC_000022.10 - 17870340	Apr 27, 2020 (154)
66	gnomAD - Genomes Submission ignored due to conflicting rows: Row 566085394 (NC_000022.11:17390450:T:C 18967/140156) Row 566085395 (NC_000022.11:17390450:T:G 1/140190)	-	Apr 27, 2021 (155)
67	gnomAD - Genomes Submission ignored due to conflicting rows: Row 566085394 (NC_000022.11:17390450:T:C 18967/140156) Row 566085395 (NC_000022.11:17390450:T:G 1/140190)	-	Apr 27, 2021 (155)
68	Genome of the Netherlands Release 5	NC_000022.10 - 17870340	Apr 27, 2020 (154)
69	KOREAN population from KRGDB	NC_000022.10 - 17870340	Apr 27, 2020 (154)
70	Northern Sweden	NC_000022.10 - 17870340	Jul 13, 2019 (153)
71	Qatari	NC_000022.10 - 17870340	Apr 27, 2020 (154)
72	SGDP_PRJ	NC_000022.10 - 17870340	Apr 27, 2020 (154)
73	Siberian	NC_000022.10 - 17870340	Apr 27, 2020 (154)
74	8.3KJPN	NC_000022.10 - 17870340	Apr 27, 2021 (155)
75	14KJPN	NC_000022.11 - 17390451	Oct 16, 2022 (156)
76	TopMed	NC_000022.11 - 17390451	Apr 27, 2021 (155)
77	UK 10K study - Twins	NC_000022.10 - 17870340	Oct 12, 2018 (152)
78	A Vietnamese Genetic Variation Database	NC_000022.10 - 17870340	Jul 13, 2019 (153)
79	ALFA	NC_000022.11 - 17390451	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
2588335161	NC_000022.11:17390450:T:A	NC_000022.11:17390450:T:A	(self)
ss112539637, ss283580288, ss484286421, ss1699275417	NC_000022.9:16250339:T:C	NC_000022.11:17390450:T:C	(self)
80153120, 44349390, 31333059, 5862612, 19758263, 47768780, 17093016, 20807068, 42231638, 11281019, 89926296, 44349390, 9785115, ss228610382, ss238016481, ss244147059, ss482994376, ss534964076, ss566550185, ss662471476, ss780115714, ss781946171, ss835598581, ss995205937, ss1082559194, ss1366621033, ss1429214174, ss1579697673, ss1639724522, ss1682718555, ss1809726485, ss1938765146, ss2030155852, ss2158764665, ss2629576178, ss2633860736, ss2704504948, ss2972793762, ss3019053126, ss3352766932, ss3628502195, ss3631813283, ss3642210337, ss3685594811, ss3743808151, ss3759211044, ss3835919162, ss3841588365, ss3890214658, ss3940591386, ss5231956989, ss5316045593, ss5440425048, ss5664199138, ss5821876936, ss5959077049	NC_000022.10:17870339:T:C	NC_000022.11:17390450:T:C	(self)
105458056, 126712348, 379715664, 2588335161, ss3028916186, ss3707922149, ss3822378190, ss3847103148, ss5104606717, ss5310601044, ss5502521677, ss5617932121, ss5792875244, ss5818579146, ss5853339922, ss5881290482	NC_000022.11:17390450:T:C	NC_000022.11:17390450:T:C	(self)
ss157012893	NT_011519.10:1022489:T:C	NC_000022.11:17390450:T:C	(self)
	NC_000022.11:17390450:T:G	NC_000022.11:17390450:T: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 rs73153492

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs73153492