Name: rs16939730
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.

rs16939730

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr17:44923113 (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=0.084850 (22459/264690, TOPMED)
T=0.048754 (7349/150736, ALFA)
T=0.07099 (2006/28258, 14KJPN) (+ 19 more)
T=0.07029 (1178/16760, 8.3KJPN)
T=0.1277 (818/6404, 1000G_30x)
T=0.1300 (651/5008, 1000G)
T=0.0527 (236/4480, Estonian)
T=0.0433 (167/3854, ALSPAC)
T=0.0361 (134/3708, TWINSUK)
T=0.1064 (311/2922, KOREAN)
T=0.1118 (233/2084, HGDP_Stanford)
T=0.1025 (194/1892, HapMap)
T=0.1135 (208/1832, Korea1K)
T=0.027 (27/998, GoNL)
T=0.013 (8/600, NorthernSweden)
T=0.116 (25/216, Qatari)
T=0.084 (18/214, Vietnamese)
C=0.490 (50/102, SGDP_PRJ)
T=0.07 (6/80, Ancient Sardinia)
T=0.03 (1/40, GENOME_DK)
C=0.5 (4/8, Siberian)
T=0.5 (4/8, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC105371793 : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	150736	C=0.951246	A=0.000000, T=0.048754
European	Sub	128118	C=0.960903	A=0.000000, T=0.039097
African	Sub	8796	C=0.9101	A=0.0000, T=0.0899
African Others	Sub	298	C=0.909	A=0.000, T=0.091
African American	Sub	8498	C=0.9101	A=0.0000, T=0.0899
Asian	Sub	610	C=0.913	A=0.000, T=0.087
East Asian	Sub	480	C=0.902	A=0.000, T=0.098
Other Asian	Sub	130	C=0.954	A=0.000, T=0.046
Latin American 1	Sub	722	C=0.945	A=0.000, T=0.055
Latin American 2	Sub	6126	C=0.8278	A=0.0000, T=0.1722
South Asian	Sub	150	C=0.820	A=0.000, T=0.180
Other	Sub	6214	C=0.9398	A=0.0000, T=0.0602

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=0.915150	T=0.084850
Allele Frequency Aggregator	Total	Global	150736	C=0.951246	A=0.000000, T=0.048754
Allele Frequency Aggregator	European	Sub	128118	C=0.960903	A=0.000000, T=0.039097
Allele Frequency Aggregator	African	Sub	8796	C=0.9101	A=0.0000, T=0.0899
Allele Frequency Aggregator	Other	Sub	6214	C=0.9398	A=0.0000, T=0.0602
Allele Frequency Aggregator	Latin American 2	Sub	6126	C=0.8278	A=0.0000, T=0.1722
Allele Frequency Aggregator	Latin American 1	Sub	722	C=0.945	A=0.000, T=0.055
Allele Frequency Aggregator	Asian	Sub	610	C=0.913	A=0.000, T=0.087
Allele Frequency Aggregator	South Asian	Sub	150	C=0.820	A=0.000, T=0.180
14KJPN	JAPANESE	Study-wide	28258	C=0.92901	T=0.07099
8.3KJPN	JAPANESE	Study-wide	16760	C=0.92971	T=0.07029
1000Genomes_30x	Global	Study-wide	6404	C=0.8723	T=0.1277
1000Genomes_30x	African	Sub	1786	C=0.8707	T=0.1293
1000Genomes_30x	Europe	Sub	1266	C=0.9660	T=0.0340
1000Genomes_30x	South Asian	Sub	1202	C=0.8003	T=0.1997
1000Genomes_30x	East Asian	Sub	1170	C=0.8436	T=0.1564
1000Genomes_30x	American	Sub	980	C=0.877	T=0.123
1000Genomes	Global	Study-wide	5008	C=0.8700	T=0.1300
1000Genomes	African	Sub	1322	C=0.8676	T=0.1324
1000Genomes	East Asian	Sub	1008	C=0.8452	T=0.1548
1000Genomes	Europe	Sub	1006	C=0.9642	T=0.0358
1000Genomes	South Asian	Sub	978	C=0.798	T=0.202
1000Genomes	American	Sub	694	C=0.876	T=0.124
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9473	T=0.0527
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9567	T=0.0433
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9639	T=0.0361
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.8936	T=0.1064
HGDP-CEPH-db Supplement 1	Global	Study-wide	2084	C=0.8882	T=0.1118
HGDP-CEPH-db Supplement 1	Est_Asia	Sub	470	C=0.894	T=0.106
HGDP-CEPH-db Supplement 1	Central_South_Asia	Sub	414	C=0.867	T=0.133
HGDP-CEPH-db Supplement 1	Middle_Est	Sub	350	C=0.929	T=0.071
HGDP-CEPH-db Supplement 1	Europe	Sub	320	C=0.969	T=0.031
HGDP-CEPH-db Supplement 1	Africa	Sub	242	C=0.843	T=0.157
HGDP-CEPH-db Supplement 1	America	Sub	216	C=0.745	T=0.255
HGDP-CEPH-db Supplement 1	Oceania	Sub	72	C=1.00	T=0.00
HapMap	Global	Study-wide	1892	C=0.8975	T=0.1025
HapMap	American	Sub	770	C=0.892	T=0.108
HapMap	African	Sub	692	C=0.900	T=0.100
HapMap	Asian	Sub	254	C=0.866	T=0.134
HapMap	Europe	Sub	176	C=0.955	T=0.045
Korean Genome Project	KOREAN	Study-wide	1832	C=0.8865	T=0.1135
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.973	T=0.027
Northern Sweden	ACPOP	Study-wide	600	C=0.987	T=0.013
Qatari	Global	Study-wide	216	C=0.884	T=0.116
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.916	T=0.084
SGDP_PRJ	Global	Study-wide	102	C=0.490	T=0.510
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	80	C=0.93	T=0.07
The Danish reference pan genome	Danish	Study-wide	40	C=0.97	T=0.03
Siberian	Global	Study-wide	8	C=0.5	T=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 17	NC_000017.11:g.44923113C>A
GRCh38.p14 chr 17	NC_000017.11:g.44923113C>T
GRCh37.p13 chr 17	NC_000017.10:g.43000481C>A
GRCh37.p13 chr 17	NC_000017.10:g.43000481C>T

Gene: LOC105371793, uncharacterized LOC105371793 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105371793 transcript	XR_934781.3:n.	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	C=	A	T
GRCh38.p14 chr 17	NC_000017.11:g.44923113=	NC_000017.11:g.44923113C>A	NC_000017.11:g.44923113C>T
GRCh37.p13 chr 17	NC_000017.10:g.43000481=	NC_000017.10:g.43000481C>A	NC_000017.10:g.43000481C>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#.

92 SubSNP, 23 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	PERLEGEN	ss24104513	Sep 20, 2004 (123)
2	ILLUMINA	ss67507789	Nov 30, 2006 (127)
3	ILLUMINA	ss71200005	May 17, 2007 (127)
4	ILLUMINA	ss75425599	Dec 07, 2007 (129)
5	ILLUMINA-UK	ss118059827	Feb 14, 2009 (130)
6	KRIBB_YJKIM	ss119854974	Dec 01, 2009 (131)
7	ILLUMINA	ss160399871	Dec 01, 2009 (131)
8	ILLUMINA	ss172670375	Jul 04, 2010 (132)
9	BUSHMAN	ss202535771	Jul 04, 2010 (132)
10	1000GENOMES	ss227554743	Jul 14, 2010 (132)
11	1000GENOMES	ss237248178	Jul 15, 2010 (132)
12	1000GENOMES	ss243545536	Jul 15, 2010 (132)
13	GMI	ss282771653	May 04, 2012 (137)
14	ILLUMINA	ss480112956	May 04, 2012 (137)
15	ILLUMINA	ss480121878	May 04, 2012 (137)
16	ILLUMINA	ss480816416	Sep 08, 2015 (146)
17	ILLUMINA	ss484854346	May 04, 2012 (137)
18	ILLUMINA	ss536922312	Sep 08, 2015 (146)
19	TISHKOFF	ss565282485	Apr 25, 2013 (138)
20	SSMP	ss661085200	Apr 25, 2013 (138)
21	ILLUMINA	ss778821578	Sep 08, 2015 (146)
22	ILLUMINA	ss782873682	Sep 08, 2015 (146)
23	ILLUMINA	ss783837674	Sep 08, 2015 (146)
24	ILLUMINA	ss832127882	Sep 08, 2015 (146)
25	ILLUMINA	ss834281929	Sep 08, 2015 (146)
26	EVA-GONL	ss993123401	Aug 21, 2014 (142)
27	JMKIDD_LAB	ss1081068796	Aug 21, 2014 (142)
28	1000GENOMES	ss1358720275	Aug 21, 2014 (142)
29	DDI	ss1428037965	Apr 01, 2015 (144)
30	EVA_GENOME_DK	ss1578162784	Apr 01, 2015 (144)
31	EVA_UK10K_ALSPAC	ss1635684413	Apr 01, 2015 (144)
32	EVA_UK10K_TWINSUK	ss1678678446	Apr 01, 2015 (144)
33	EVA_DECODE	ss1697166858	Apr 01, 2015 (144)
34	EVA_SVP	ss1713583568	Apr 01, 2015 (144)
35	ILLUMINA	ss1752227008	Sep 08, 2015 (146)
36	HAMMER_LAB	ss1808789636	Sep 08, 2015 (146)
37	WEILL_CORNELL_DGM	ss1936583948	Feb 12, 2016 (147)
38	JJLAB	ss2029068368	Sep 14, 2016 (149)
39	USC_VALOUEV	ss2157540539	Dec 20, 2016 (150)
40	HUMAN_LONGEVITY	ss2216975702	Dec 20, 2016 (150)
41	SYSTEMSBIOZJU	ss2629030337	Nov 08, 2017 (151)
42	ILLUMINA	ss2633398642	Nov 08, 2017 (151)
43	GRF	ss2702102931	Nov 08, 2017 (151)
44	GNOMAD	ss2950064885	Nov 08, 2017 (151)
45	AFFY	ss2985731889	Nov 08, 2017 (151)
46	SWEGEN	ss3015562025	Nov 08, 2017 (151)
47	BIOINF_KMB_FNS_UNIBA	ss3028354513	Nov 08, 2017 (151)
48	CSHL	ss3351753280	Nov 08, 2017 (151)
49	ILLUMINA	ss3627673781	Oct 12, 2018 (152)
50	ILLUMINA	ss3631379609	Oct 12, 2018 (152)
51	ILLUMINA	ss3633142042	Oct 12, 2018 (152)
52	ILLUMINA	ss3633849612	Oct 12, 2018 (152)
53	ILLUMINA	ss3634676458	Oct 12, 2018 (152)
54	ILLUMINA	ss3635537357	Oct 12, 2018 (152)
55	ILLUMINA	ss3636366005	Oct 12, 2018 (152)
56	ILLUMINA	ss3637288908	Oct 12, 2018 (152)
57	ILLUMINA	ss3638162648	Oct 12, 2018 (152)
58	ILLUMINA	ss3640383770	Oct 12, 2018 (152)
59	ILLUMINA	ss3643140976	Oct 12, 2018 (152)
60	EGCUT_WGS	ss3682447500	Jul 13, 2019 (153)
61	EVA_DECODE	ss3700499266	Jul 13, 2019 (153)
62	ACPOP	ss3742039031	Jul 13, 2019 (153)
63	ILLUMINA	ss3744976752	Jul 13, 2019 (153)
64	EVA	ss3754685758	Jul 13, 2019 (153)
65	ILLUMINA	ss3772474611	Jul 13, 2019 (153)
66	KHV_HUMAN_GENOMES	ss3819954717	Jul 13, 2019 (153)
67	EVA	ss3834875137	Apr 27, 2020 (154)
68	HGDP	ss3847564443	Apr 27, 2020 (154)
69	SGDP_PRJ	ss3885782390	Apr 27, 2020 (154)
70	KRGDB	ss3935478288	Apr 27, 2020 (154)
71	KOGIC	ss3978881866	Apr 27, 2020 (154)
72	EVA	ss3985791909	Apr 27, 2021 (155)
73	EVA	ss4017767841	Apr 27, 2021 (155)
74	TOPMED	ss5036570969	Apr 27, 2021 (155)
75	TOMMO_GENOMICS	ss5222496331	Apr 27, 2021 (155)
76	EVA	ss5237575807	Apr 27, 2021 (155)
77	1000G_HIGH_COVERAGE	ss5303192012	Oct 16, 2022 (156)
78	EVA	ss5315887653	Oct 16, 2022 (156)
79	EVA	ss5427700614	Oct 16, 2022 (156)
80	HUGCELL_USP	ss5496241702	Oct 16, 2022 (156)
81	1000G_HIGH_COVERAGE	ss5606939788	Oct 16, 2022 (156)
82	SANFORD_IMAGENETICS	ss5624397568	Oct 16, 2022 (156)
83	SANFORD_IMAGENETICS	ss5660135122	Oct 16, 2022 (156)
84	TOMMO_GENOMICS	ss5778734614	Oct 16, 2022 (156)
85	EVA	ss5799975998	Oct 16, 2022 (156)
86	YY_MCH	ss5816556189	Oct 16, 2022 (156)
87	EVA	ss5834005864	Oct 16, 2022 (156)
88	EVA	ss5847474975	Oct 16, 2022 (156)
89	EVA	ss5847798794	Oct 16, 2022 (156)
90	EVA	ss5914023346	Oct 16, 2022 (156)
91	EVA	ss5951528038	Oct 16, 2022 (156)
92	EVA	ss5979507831	Oct 16, 2022 (156)
93	1000Genomes	NC_000017.10 - 43000481	Oct 12, 2018 (152)
94	1000Genomes_30x	NC_000017.11 - 44923113	Oct 16, 2022 (156)
95	The Avon Longitudinal Study of Parents and Children	NC_000017.10 - 43000481	Oct 12, 2018 (152)
96	Genetic variation in the Estonian population	NC_000017.10 - 43000481	Oct 12, 2018 (152)
97	The Danish reference pan genome	NC_000017.10 - 43000481	Apr 27, 2020 (154)
98	gnomAD - Genomes Submission ignored due to conflicting rows: Row 507745922 (NC_000017.11:44923112:C:A 1/140196) Row 507745923 (NC_000017.11:44923112:C:T 10279/140176)	-	Apr 27, 2021 (155)
99	gnomAD - Genomes Submission ignored due to conflicting rows: Row 507745922 (NC_000017.11:44923112:C:A 1/140196) Row 507745923 (NC_000017.11:44923112:C:T 10279/140176)	-	Apr 27, 2021 (155)
100	Genome of the Netherlands Release 5	NC_000017.10 - 43000481	Apr 27, 2020 (154)
101	HGDP-CEPH-db Supplement 1	NC_000017.9 - 40356007	Apr 27, 2020 (154)
102	HapMap	NC_000017.11 - 44923113	Apr 27, 2020 (154)
103	KOREAN population from KRGDB	NC_000017.10 - 43000481	Apr 27, 2020 (154)
104	Korean Genome Project	NC_000017.11 - 44923113	Apr 27, 2020 (154)
105	Northern Sweden	NC_000017.10 - 43000481	Jul 13, 2019 (153)
106	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000017.10 - 43000481	Apr 27, 2021 (155)
107	Qatari	NC_000017.10 - 43000481	Apr 27, 2020 (154)
108	SGDP_PRJ	NC_000017.10 - 43000481	Apr 27, 2020 (154)
109	Siberian	NC_000017.10 - 43000481	Apr 27, 2020 (154)
110	8.3KJPN	NC_000017.10 - 43000481	Apr 27, 2021 (155)
111	14KJPN	NC_000017.11 - 44923113	Oct 16, 2022 (156)
112	TopMed	NC_000017.11 - 44923113	Apr 27, 2021 (155)
113	UK 10K study - Twins	NC_000017.10 - 43000481	Oct 12, 2018 (152)
114	A Vietnamese Genetic Variation Database	NC_000017.10 - 43000481	Jul 13, 2019 (153)
115	ALFA	NC_000017.11 - 44923113	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
2840886848	NC_000017.11:44923112:C:A	NC_000017.11:44923112:C:A	(self)
242335, ss118059827, ss202535771, ss282771653, ss480112956, ss1697166858, ss1713583568, ss3643140976, ss3847564443	NC_000017.9:40356006:C:T	NC_000017.11:44923112:C:T	(self)
71964509, 39883866, 28185748, 4364980, 17774580, 42655682, 15323896, 1017836, 18625870, 37799370, 10056893, 80465638, 39883866, 8824261, ss227554743, ss237248178, ss243545536, ss480121878, ss480816416, ss484854346, ss536922312, ss565282485, ss661085200, ss778821578, ss782873682, ss783837674, ss832127882, ss834281929, ss993123401, ss1081068796, ss1358720275, ss1428037965, ss1578162784, ss1635684413, ss1678678446, ss1752227008, ss1808789636, ss1936583948, ss2029068368, ss2157540539, ss2629030337, ss2633398642, ss2702102931, ss2950064885, ss2985731889, ss3015562025, ss3351753280, ss3627673781, ss3631379609, ss3633142042, ss3633849612, ss3634676458, ss3635537357, ss3636366005, ss3637288908, ss3638162648, ss3640383770, ss3682447500, ss3742039031, ss3744976752, ss3754685758, ss3772474611, ss3834875137, ss3885782390, ss3935478288, ss3985791909, ss4017767841, ss5222496331, ss5237575807, ss5315887653, ss5427700614, ss5624397568, ss5660135122, ss5799975998, ss5834005864, ss5847474975, ss5847798794, ss5951528038, ss5979507831	NC_000017.10:43000480:C:T	NC_000017.11:44923112:C:T	(self)
94465723, 1490541, 35259867, 112571718, 252116631, 2840886848, ss2216975702, ss3028354513, ss3700499266, ss3819954717, ss3978881866, ss5036570969, ss5303192012, ss5496241702, ss5606939788, ss5778734614, ss5816556189, ss5914023346	NC_000017.11:44923112:C:T	NC_000017.11:44923112:C:T	(self)
ss24104513, ss67507789, ss71200005, ss75425599, ss119854974, ss160399871, ss172670375	NT_010783.15:8274632:C:T	NC_000017.11:44923112: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 rs16939730

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

rs16939730