Name: rs17002369
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.

rs17002369

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr22:41234245 (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: G>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.081235 (21502/264690, TOPMED)
C=0.071803 (10063/140148, GnomAD)
C=0.03185 (900/28258, 14KJPN) (+ 15 more)
C=0.03240 (543/16760, 8.3KJPN)
C=0.05298 (764/14420, ALFA)
C=0.0828 (530/6404, 1000G_30x)
C=0.0789 (395/5008, 1000G)
C=0.0016 (6/3854, ALSPAC)
C=0.0019 (7/3708, TWINSUK)
C=0.0287 (84/2930, KOREAN)
C=0.0300 (55/1832, Korea1K)
C=0.004 (4/998, GoNL)
C=0.100 (33/330, HapMap)
C=0.074 (16/216, Qatari)
C=0.023 (5/214, Vietnamese)
G=0.44 (31/70, SGDP_PRJ)
G=0.5 (1/2, Siberian)
C=0.5 (1/2, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CHADL : 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	14420	G=0.94702	C=0.05298
European	Sub	9824	G=0.9968	C=0.0032
African	Sub	2946	G=0.7895	C=0.2105
African Others	Sub	114	G=0.816	C=0.184
African American	Sub	2832	G=0.7885	C=0.2115
Asian	Sub	112	G=1.000	C=0.000
East Asian	Sub	86	G=1.00	C=0.00
Other Asian	Sub	26	G=1.00	C=0.00
Latin American 1	Sub	146	G=0.890	C=0.110
Latin American 2	Sub	610	G=0.913	C=0.087
South Asian	Sub	98	G=0.99	C=0.01
Other	Sub	684	G=0.937	C=0.063

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	G=0.918765	C=0.081235
gnomAD - Genomes	Global	Study-wide	140148	G=0.928197	C=0.071803
gnomAD - Genomes	European	Sub	75926	G=0.99802	C=0.00198
gnomAD - Genomes	African	Sub	41966	G=0.80122	C=0.19878
gnomAD - Genomes	American	Sub	13650	G=0.90425	C=0.09575
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	G=0.9868	C=0.0132
gnomAD - Genomes	East Asian	Sub	3132	G=0.9792	C=0.0208
gnomAD - Genomes	Other	Sub	2152	G=0.9280	C=0.0720
14KJPN	JAPANESE	Study-wide	28258	G=0.96815	C=0.03185
8.3KJPN	JAPANESE	Study-wide	16760	G=0.96760	C=0.03240
Allele Frequency Aggregator	Total	Global	14420	G=0.94702	C=0.05298
Allele Frequency Aggregator	European	Sub	9824	G=0.9968	C=0.0032
Allele Frequency Aggregator	African	Sub	2946	G=0.7895	C=0.2105
Allele Frequency Aggregator	Other	Sub	684	G=0.937	C=0.063
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.913	C=0.087
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.890	C=0.110
Allele Frequency Aggregator	Asian	Sub	112	G=1.000	C=0.000
Allele Frequency Aggregator	South Asian	Sub	98	G=0.99	C=0.01
1000Genomes_30x	Global	Study-wide	6404	G=0.9172	C=0.0828
1000Genomes_30x	African	Sub	1786	G=0.7861	C=0.2139
1000Genomes_30x	Europe	Sub	1266	G=0.9961	C=0.0039
1000Genomes_30x	South Asian	Sub	1202	G=0.9992	C=0.0008
1000Genomes_30x	East Asian	Sub	1170	G=0.9744	C=0.0256
1000Genomes_30x	American	Sub	980	G=0.886	C=0.114
1000Genomes	Global	Study-wide	5008	G=0.9211	C=0.0789
1000Genomes	African	Sub	1322	G=0.7874	C=0.2126
1000Genomes	East Asian	Sub	1008	G=0.9762	C=0.0238
1000Genomes	Europe	Sub	1006	G=0.9960	C=0.0040
1000Genomes	South Asian	Sub	978	G=0.999	C=0.001
1000Genomes	American	Sub	694	G=0.878	C=0.122
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9984	C=0.0016
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9981	C=0.0019
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.9713	C=0.0287
Korean Genome Project	KOREAN	Study-wide	1832	G=0.9700	C=0.0300
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.996	C=0.004
HapMap	Global	Study-wide	330	G=0.900	C=0.100
HapMap	African	Sub	120	G=0.742	C=0.258
HapMap	American	Sub	120	G=1.000	C=0.000
HapMap	Asian	Sub	90	G=0.98	C=0.02
Qatari	Global	Study-wide	216	G=0.926	C=0.074
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.977	C=0.023
SGDP_PRJ	Global	Study-wide	70	G=0.44	C=0.56
Siberian	Global	Study-wide	2	G=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 22	NC_000022.11:g.41234245G>C
GRCh37.p13 chr 22	NC_000022.10:g.41630249G>C

Gene: CHADL, chondroadherin like (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CHADL transcript	NM_138481.2:c.2262+900C>G	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	G=	C
GRCh38.p14 chr 22	NC_000022.11:g.41234245=	NC_000022.11:g.41234245G>C
GRCh37.p13 chr 22	NC_000022.10:g.41630249=	NC_000022.10:g.41630249G>C
CHADL transcript	NM_138481.1:c.2262+900=	NM_138481.1:c.2262+900C>G
CHADL transcript	NM_138481.2:c.2262+900=	NM_138481.2:c.2262+900C>G
CHADL transcript variant X1	XM_005261370.1:c.2262+900=	XM_005261370.1:c.2262+900C>G
CHADL transcript variant X2	XM_005261371.1:c.2262+900=	XM_005261371.1:c.2262+900C>G
CHADL transcript variant X3	XM_005261372.1:c.2034+900=	XM_005261372.1:c.2034+900C>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#.

43 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	PERLEGEN	ss23571568	Sep 20, 2004 (123)
2	HGSV	ss84596764	Dec 14, 2007 (130)
3	1000GENOMES	ss114248247	Jan 25, 2009 (130)
4	ILLUMINA-UK	ss117414668	Feb 14, 2009 (130)
5	BUSHMAN	ss204098144	Jul 04, 2010 (132)
6	1000GENOMES	ss228695955	Jul 14, 2010 (132)
7	GMI	ss283647357	May 04, 2012 (137)
8	TISHKOFF	ss566663465	Apr 25, 2013 (138)
9	SSMP	ss662592837	Apr 25, 2013 (138)
10	EVA-GONL	ss995387893	Aug 21, 2014 (142)
11	JMKIDD_LAB	ss1082683858	Aug 21, 2014 (142)
12	1000GENOMES	ss1367311800	Aug 21, 2014 (142)
13	EVA_UK10K_ALSPAC	ss1640071131	Apr 01, 2015 (144)
14	EVA_UK10K_TWINSUK	ss1683065164	Apr 01, 2015 (144)
15	EVA_DECODE	ss1699459061	Apr 01, 2015 (144)
16	WEILL_CORNELL_DGM	ss1938955547	Feb 12, 2016 (147)
17	GENOMED	ss1969278657	Jul 19, 2016 (147)
18	JJLAB	ss2030250325	Sep 14, 2016 (149)
19	USC_VALOUEV	ss2158870337	Dec 20, 2016 (150)
20	HUMAN_LONGEVITY	ss2247635352	Dec 20, 2016 (150)
21	GRF	ss2704623252	Nov 08, 2017 (151)
22	GNOMAD	ss2974816712	Nov 08, 2017 (151)
23	SWEGEN	ss3019364806	Nov 08, 2017 (151)
24	EVA_DECODE	ss3708275093	Jul 13, 2019 (153)
25	EVA	ss3759427412	Jul 13, 2019 (153)
26	KHV_HUMAN_GENOMES	ss3822587461	Jul 13, 2019 (153)
27	EVA	ss3836009609	Apr 27, 2020 (154)
28	SGDP_PRJ	ss3890625506	Apr 27, 2020 (154)
29	KRGDB	ss3941018308	Apr 27, 2020 (154)
30	KOGIC	ss3983719983	Apr 27, 2020 (154)
31	TOPMED	ss5110544841	Apr 26, 2021 (155)
32	TOMMO_GENOMICS	ss5232805583	Apr 26, 2021 (155)
33	1000G_HIGH_COVERAGE	ss5311233464	Oct 16, 2022 (156)
34	EVA	ss5441546823	Oct 16, 2022 (156)
35	HUGCELL_USP	ss5503063496	Oct 16, 2022 (156)
36	EVA	ss5512390435	Oct 16, 2022 (156)
37	1000G_HIGH_COVERAGE	ss5618851647	Oct 16, 2022 (156)
38	SANFORD_IMAGENETICS	ss5664565046	Oct 16, 2022 (156)
39	TOMMO_GENOMICS	ss5793986346	Oct 16, 2022 (156)
40	YY_MCH	ss5818743449	Oct 16, 2022 (156)
41	EVA	ss5822123177	Oct 16, 2022 (156)
42	EVA	ss5881970524	Oct 16, 2022 (156)
43	EVA	ss5959423253	Oct 16, 2022 (156)
44	1000Genomes	NC_000022.10 - 41630249	Oct 12, 2018 (152)
45	1000Genomes_30x	NC_000022.11 - 41234245	Oct 16, 2022 (156)
46	The Avon Longitudinal Study of Parents and Children	NC_000022.10 - 41630249	Oct 12, 2018 (152)
47	gnomAD - Genomes	NC_000022.11 - 41234245	Apr 26, 2021 (155)
48	Genome of the Netherlands Release 5	NC_000022.10 - 41630249	Apr 27, 2020 (154)
49	HapMap	NC_000022.11 - 41234245	Apr 27, 2020 (154)
50	KOREAN population from KRGDB	NC_000022.10 - 41630249	Apr 27, 2020 (154)
51	Korean Genome Project	NC_000022.11 - 41234245	Apr 27, 2020 (154)
52	Qatari	NC_000022.10 - 41630249	Apr 27, 2020 (154)
53	SGDP_PRJ	NC_000022.10 - 41630249	Apr 27, 2020 (154)
54	Siberian	NC_000022.10 - 41630249	Apr 27, 2020 (154)
55	8.3KJPN	NC_000022.10 - 41630249	Apr 26, 2021 (155)
56	14KJPN	NC_000022.11 - 41234245	Oct 16, 2022 (156)
57	TopMed	NC_000022.11 - 41234245	Apr 26, 2021 (155)
58	UK 10K study - Twins	NC_000022.10 - 41630249	Oct 12, 2018 (152)
59	A Vietnamese Genetic Variation Database	NC_000022.10 - 41630249	Jul 13, 2019 (153)
60	ALFA	NC_000022.11 - 41234245	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)
rs57391650	May 23, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss84596764	NC_000022.8:39954748:G:C	NC_000022.11:41234244:G:C	(self)
ss114248247, ss117414668, ss204098144, ss283647357, ss1699459061	NC_000022.9:39960194:G:C	NC_000022.11:41234244:G:C	(self)
80869337, 44733618, 19930389, 48195702, 20997469, 42642486, 11386691, 90774890, 44733618, 9866192, ss228695955, ss566663465, ss662592837, ss995387893, ss1082683858, ss1367311800, ss1640071131, ss1683065164, ss1938955547, ss1969278657, ss2030250325, ss2158870337, ss2704623252, ss2974816712, ss3019364806, ss3759427412, ss3836009609, ss3890625506, ss3941018308, ss5232805583, ss5441546823, ss5512390435, ss5664565046, ss5822123177, ss5959423253	NC_000022.10:41630248:G:C	NC_000022.11:41234244:G:C	(self)
106377582, 571074180, 2262437, 40097984, 127823450, 385653788, 10794382631, ss2247635352, ss3708275093, ss3822587461, ss3983719983, ss5110544841, ss5311233464, ss5503063496, ss5618851647, ss5793986346, ss5818743449, ss5881970524	NC_000022.11:41234244:G:C	NC_000022.11:41234244:G:C	(self)
ss23571568	NT_011520.12:21020817:G:C	NC_000022.11:41234244:G: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 rs17002369

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

rs17002369