Name: rs17419765
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.

rs17419765

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:123742891 (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=0.175466 (46444/264690, TOPMED)
C=0.176271 (24679/140006, GnomAD)
C=0.17691 (8558/48376, ALFA) (+ 18 more)
C=0.12630 (3569/28258, 14KJPN)
C=0.12482 (2092/16760, 8.3KJPN)
C=0.1374 (880/6404, 1000G_30x)
C=0.1364 (683/5008, 1000G)
C=0.1455 (652/4480, Estonian)
C=0.1941 (748/3854, ALSPAC)
C=0.2087 (774/3708, TWINSUK)
C=0.1010 (296/2930, KOREAN)
C=0.0868 (159/1832, Korea1K)
C=0.188 (188/998, GoNL)
C=0.215 (129/600, NorthernSweden)
C=0.155 (51/330, HapMap)
C=0.130 (28/216, Qatari)
C=0.028 (6/216, Vietnamese)
T=0.466 (54/116, SGDP_PRJ)
C=0.07 (3/40, GENOME_DK)
T=0.50 (6/12, Siberian)
C=0.50 (6/12, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
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	48376	T=0.82309	C=0.17691
European	Sub	34120	T=0.81114	C=0.18886
African	Sub	4938	T=0.8404	C=0.1596
African Others	Sub	180	T=0.828	C=0.172
African American	Sub	4758	T=0.8409	C=0.1591
Asian	Sub	438	T=0.916	C=0.084
East Asian	Sub	372	T=0.901	C=0.099
Other Asian	Sub	66	T=1.00	C=0.00
Latin American 1	Sub	574	T=0.828	C=0.172
Latin American 2	Sub	4900	T=0.8851	C=0.1149
South Asian	Sub	162	T=0.914	C=0.086
Other	Sub	3244	T=0.8110	C=0.1890

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=0.824534	C=0.175466
gnomAD - Genomes	Global	Study-wide	140006	T=0.823729	C=0.176271
gnomAD - Genomes	European	Sub	75852	T=0.81199	C=0.18801
gnomAD - Genomes	African	Sub	41932	T=0.84282	C=0.15718
gnomAD - Genomes	American	Sub	13636	T=0.82847	C=0.17153
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=0.7461	C=0.2539
gnomAD - Genomes	East Asian	Sub	3118	T=0.9163	C=0.0837
gnomAD - Genomes	Other	Sub	2148	T=0.8212	C=0.1788
Allele Frequency Aggregator	Total	Global	48376	T=0.82309	C=0.17691
Allele Frequency Aggregator	European	Sub	34120	T=0.81114	C=0.18886
Allele Frequency Aggregator	African	Sub	4938	T=0.8404	C=0.1596
Allele Frequency Aggregator	Latin American 2	Sub	4900	T=0.8851	C=0.1149
Allele Frequency Aggregator	Other	Sub	3244	T=0.8110	C=0.1890
Allele Frequency Aggregator	Latin American 1	Sub	574	T=0.828	C=0.172
Allele Frequency Aggregator	Asian	Sub	438	T=0.916	C=0.084
Allele Frequency Aggregator	South Asian	Sub	162	T=0.914	C=0.086
14KJPN	JAPANESE	Study-wide	28258	T=0.87370	C=0.12630
8.3KJPN	JAPANESE	Study-wide	16760	T=0.87518	C=0.12482
1000Genomes_30x	Global	Study-wide	6404	T=0.8626	C=0.1374
1000Genomes_30x	African	Sub	1786	T=0.8292	C=0.1708
1000Genomes_30x	Europe	Sub	1266	T=0.8009	C=0.1991
1000Genomes_30x	South Asian	Sub	1202	T=0.9052	C=0.0948
1000Genomes_30x	East Asian	Sub	1170	T=0.9248	C=0.0752
1000Genomes_30x	American	Sub	980	T=0.877	C=0.123
1000Genomes	Global	Study-wide	5008	T=0.8636	C=0.1364
1000Genomes	African	Sub	1322	T=0.8298	C=0.1702
1000Genomes	East Asian	Sub	1008	T=0.9246	C=0.0754
1000Genomes	Europe	Sub	1006	T=0.8042	C=0.1958
1000Genomes	South Asian	Sub	978	T=0.902	C=0.098
1000Genomes	American	Sub	694	T=0.872	C=0.128
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.8545	C=0.1455
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.8059	C=0.1941
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.7913	C=0.2087
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.8990	C=0.1010
Korean Genome Project	KOREAN	Study-wide	1832	T=0.9132	C=0.0868
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.812	C=0.188
Northern Sweden	ACPOP	Study-wide	600	T=0.785	C=0.215
HapMap	Global	Study-wide	330	T=0.845	C=0.155
HapMap	African	Sub	120	T=0.833	C=0.167
HapMap	American	Sub	120	T=0.825	C=0.175
HapMap	Asian	Sub	90	T=0.89	C=0.11
Qatari	Global	Study-wide	216	T=0.870	C=0.130
A Vietnamese Genetic Variation Database	Global	Study-wide	216	T=0.972	C=0.028
SGDP_PRJ	Global	Study-wide	116	T=0.466	C=0.534
The Danish reference pan genome	Danish	Study-wide	40	T=0.93	C=0.07
Siberian	Global	Study-wide	12	T=0.50	C=0.50

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 5	NC_000005.10:g.123742891T>C
GRCh37.p13 chr 5	NC_000005.9:g.123078585T>C

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 5	NC_000005.10:g.123742891=	NC_000005.10:g.123742891T>C
GRCh37.p13 chr 5	NC_000005.9:g.123078585=	NC_000005.9:g.123078585T>C

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#.

62 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	PERLEGEN	ss24349864	Sep 20, 2004 (123)
2	AFFY	ss66274542	Jul 04, 2010 (132)
3	PERLEGEN	ss68948356	May 17, 2007 (127)
4	AFFY	ss75924916	Dec 07, 2007 (129)
5	KRIBB_YJKIM	ss83244338	Dec 15, 2007 (130)
6	HGSV	ss84630741	Dec 16, 2007 (130)
7	ILLUMINA	ss160442983	Dec 01, 2009 (131)
8	COMPLETE_GENOMICS	ss162626045	Jul 04, 2010 (132)
9	AFFY	ss169199368	Jul 04, 2010 (132)
10	1000GENOMES	ss221936421	Jul 14, 2010 (132)
11	1000GENOMES	ss233129834	Jul 14, 2010 (132)
12	1000GENOMES	ss240254347	Jul 15, 2010 (132)
13	BL	ss253776553	May 09, 2011 (134)
14	GMI	ss278462130	May 04, 2012 (137)
15	ILLUMINA	ss480988041	Sep 08, 2015 (146)
16	TISHKOFF	ss558680885	Apr 25, 2013 (138)
17	SSMP	ss652576301	Apr 25, 2013 (138)
18	EVA-GONL	ss982068807	Aug 21, 2014 (142)
19	JMKIDD_LAB	ss1073001987	Aug 21, 2014 (142)
20	1000GENOMES	ss1317001900	Aug 21, 2014 (142)
21	DDI	ss1430487593	Apr 01, 2015 (144)
22	EVA_GENOME_DK	ss1581330209	Apr 01, 2015 (144)
23	EVA_DECODE	ss1591593211	Apr 01, 2015 (144)
24	EVA_UK10K_ALSPAC	ss1613895946	Apr 01, 2015 (144)
25	EVA_UK10K_TWINSUK	ss1656889979	Apr 01, 2015 (144)
26	EVA_SVP	ss1712796400	Apr 01, 2015 (144)
27	HAMMER_LAB	ss1804059153	Sep 08, 2015 (146)
28	WEILL_CORNELL_DGM	ss1925324807	Feb 12, 2016 (147)
29	JJLAB	ss2023268155	Sep 14, 2016 (149)
30	USC_VALOUEV	ss2151424436	Dec 20, 2016 (150)
31	HUMAN_LONGEVITY	ss2277698577	Dec 20, 2016 (150)
32	SYSTEMSBIOZJU	ss2626122737	Nov 08, 2017 (151)
33	GRF	ss2706984520	Nov 08, 2017 (151)
34	GNOMAD	ss2830153468	Nov 08, 2017 (151)
35	SWEGEN	ss2997707920	Nov 08, 2017 (151)
36	BIOINF_KMB_FNS_UNIBA	ss3025417166	Nov 08, 2017 (151)
37	CSHL	ss3346604452	Nov 08, 2017 (151)
38	ILLUMINA	ss3636732942	Oct 12, 2018 (152)
39	EGCUT_WGS	ss3665616714	Jul 13, 2019 (153)
40	EVA_DECODE	ss3715598414	Jul 13, 2019 (153)
41	ACPOP	ss3732771800	Jul 13, 2019 (153)
42	EVA	ss3763996793	Jul 13, 2019 (153)
43	PACBIO	ss3785236447	Jul 13, 2019 (153)
44	PACBIO	ss3790622624	Jul 13, 2019 (153)
45	PACBIO	ss3795499497	Jul 13, 2019 (153)
46	KHV_HUMAN_GENOMES	ss3807170754	Jul 13, 2019 (153)
47	EVA	ss3829479371	Apr 26, 2020 (154)
48	SGDP_PRJ	ss3862867752	Apr 26, 2020 (154)
49	KRGDB	ss3909493090	Apr 26, 2020 (154)
50	KOGIC	ss3957551277	Apr 26, 2020 (154)
51	TOPMED	ss4676820036	Apr 26, 2021 (155)
52	TOMMO_GENOMICS	ss5173898148	Apr 26, 2021 (155)
53	1000G_HIGH_COVERAGE	ss5265653485	Oct 17, 2022 (156)
54	HUGCELL_USP	ss5463641942	Oct 17, 2022 (156)
55	EVA	ss5508194853	Oct 17, 2022 (156)
56	1000G_HIGH_COVERAGE	ss5550205045	Oct 17, 2022 (156)
57	SANFORD_IMAGENETICS	ss5638775628	Oct 17, 2022 (156)
58	TOMMO_GENOMICS	ss5710904507	Oct 17, 2022 (156)
59	YY_MCH	ss5806721750	Oct 17, 2022 (156)
60	EVA	ss5835570527	Oct 17, 2022 (156)
61	EVA	ss5896102818	Oct 17, 2022 (156)
62	EVA	ss5967235738	Oct 17, 2022 (156)
63	1000Genomes	NC_000005.9 - 123078585	Oct 12, 2018 (152)
64	1000Genomes_30x	NC_000005.10 - 123742891	Oct 17, 2022 (156)
65	The Avon Longitudinal Study of Parents and Children	NC_000005.9 - 123078585	Oct 12, 2018 (152)
66	Genetic variation in the Estonian population	NC_000005.9 - 123078585	Oct 12, 2018 (152)
67	The Danish reference pan genome	NC_000005.9 - 123078585	Apr 26, 2020 (154)
68	gnomAD - Genomes	NC_000005.10 - 123742891	Apr 26, 2021 (155)
69	Genome of the Netherlands Release 5	NC_000005.9 - 123078585	Apr 26, 2020 (154)
70	HapMap	NC_000005.10 - 123742891	Apr 26, 2020 (154)
71	KOREAN population from KRGDB	NC_000005.9 - 123078585	Apr 26, 2020 (154)
72	Korean Genome Project	NC_000005.10 - 123742891	Apr 26, 2020 (154)
73	Northern Sweden	NC_000005.9 - 123078585	Jul 13, 2019 (153)
74	Qatari	NC_000005.9 - 123078585	Apr 26, 2020 (154)
75	SGDP_PRJ	NC_000005.9 - 123078585	Apr 26, 2020 (154)
76	Siberian	NC_000005.9 - 123078585	Apr 26, 2020 (154)
77	8.3KJPN	NC_000005.9 - 123078585	Apr 26, 2021 (155)
78	14KJPN	NC_000005.10 - 123742891	Oct 17, 2022 (156)
79	TopMed	NC_000005.10 - 123742891	Apr 26, 2021 (155)
80	UK 10K study - Twins	NC_000005.9 - 123078585	Oct 12, 2018 (152)
81	A Vietnamese Genetic Variation Database	NC_000005.9 - 123078585	Jul 13, 2019 (153)
82	ALFA	NC_000005.10 - 123742891	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)
rs59649934	Feb 27, 2009 (130)
rs61057631	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss75924916, ss84630741, ss160442983, ss162626045, ss169199368, ss253776553, ss278462130, ss1591593211, ss1712796400	NC_000005.8:123106483:T:C	NC_000005.10:123742890:T:C	(self)
28672629, 15944847, 11354962, 7495148, 7089151, 16670484, 6056665, 7366737, 14884732, 3940790, 31867455, 15944847, 3537532, ss221936421, ss233129834, ss240254347, ss480988041, ss558680885, ss652576301, ss982068807, ss1073001987, ss1317001900, ss1430487593, ss1581330209, ss1613895946, ss1656889979, ss1804059153, ss1925324807, ss2023268155, ss2151424436, ss2626122737, ss2706984520, ss2830153468, ss2997707920, ss3346604452, ss3636732942, ss3665616714, ss3732771800, ss3763996793, ss3785236447, ss3790622624, ss3795499497, ss3829479371, ss3862867752, ss3909493090, ss5173898148, ss5508194853, ss5638775628, ss5835570527, ss5967235738	NC_000005.9:123078584:T:C	NC_000005.10:123742890:T:C	(self)
37730980, 202798214, 2958278, 13929278, 44741611, 514197593, 14179958206, ss2277698577, ss3025417166, ss3715598414, ss3807170754, ss3957551277, ss4676820036, ss5265653485, ss5463641942, ss5550205045, ss5710904507, ss5806721750, ss5896102818	NC_000005.10:123742890:T:C	NC_000005.10:123742890:T:C	(self)
ss24349864, ss68948356, ss83244338	NT_034772.6:31392456:T:C	NC_000005.10:123742890:T:C	(self)
ss66274542	NT_034772.7:73633083:T:C	NC_000005.10:123742890: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 rs17419765

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

rs17419765