Name: rs1959785
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.

rs1959785

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr14:25790383 (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=0.401190 (106191/264690, TOPMED)
C=0.24202 (6839/28258, 14KJPN)
C=0.24385 (4087/16760, 8.3KJPN) (+ 14 more)
C=0.19716 (2336/11848, ALFA)
C=0.3766 (2412/6404, 1000G_30x)
C=0.3672 (1839/5008, 1000G)
C=0.3321 (1488/4480, Estonian)
C=0.2055 (602/2930, KOREAN)
C=0.1938 (355/1832, Korea1K)
C=0.318 (317/998, GoNL)
C=0.368 (221/600, NorthernSweden)
C=0.451 (147/326, HapMap)
T=0.348 (96/276, SGDP_PRJ)
C=0.227 (49/216, Qatari)
C=0.125 (27/216, Vietnamese)
C=0.35 (14/40, GENOME_DK)
T=0.43 (12/28, 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	11848	T=0.80284	A=0.00000, C=0.19716, G=0.00000
European	Sub	10476	T=0.79334	A=0.00000, C=0.20666, G=0.00000
African	Sub	472	T=0.809	A=0.000, C=0.191, G=0.000
African Others	Sub	20	T=0.70	A=0.00, C=0.30, G=0.00
African American	Sub	452	T=0.814	A=0.000, C=0.186, G=0.000
Asian	Sub	76	T=1.00	A=0.00, C=0.00, G=0.00
East Asian	Sub	60	T=1.00	A=0.00, C=0.00, G=0.00
Other Asian	Sub	16	T=1.00	A=0.00, C=0.00, G=0.00
Latin American 1	Sub	60	T=1.00	A=0.00, C=0.00, G=0.00
Latin American 2	Sub	330	T=1.000	A=0.000, C=0.000, G=0.000
South Asian	Sub	38	T=0.97	A=0.00, C=0.03, G=0.00
Other	Sub	396	T=0.798	A=0.000, C=0.202, G=0.000

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=0.598810	C=0.401190
14KJPN	JAPANESE	Study-wide	28258	T=0.75798	C=0.24202
8.3KJPN	JAPANESE	Study-wide	16760	T=0.75615	C=0.24385
Allele Frequency Aggregator	Total	Global	11848	T=0.80284	A=0.00000, C=0.19716, G=0.00000
Allele Frequency Aggregator	European	Sub	10476	T=0.79334	A=0.00000, C=0.20666, G=0.00000
Allele Frequency Aggregator	African	Sub	472	T=0.809	A=0.000, C=0.191, G=0.000
Allele Frequency Aggregator	Other	Sub	396	T=0.798	A=0.000, C=0.202, G=0.000
Allele Frequency Aggregator	Latin American 2	Sub	330	T=1.000	A=0.000, C=0.000, G=0.000
Allele Frequency Aggregator	Asian	Sub	76	T=1.00	A=0.00, C=0.00, G=0.00
Allele Frequency Aggregator	Latin American 1	Sub	60	T=1.00	A=0.00, C=0.00, G=0.00
Allele Frequency Aggregator	South Asian	Sub	38	T=0.97	A=0.00, C=0.03, G=0.00
1000Genomes_30x	Global	Study-wide	6404	T=0.6230	A=0.0003, C=0.3766
1000Genomes_30x	African	Sub	1786	T=0.3147	A=0.0000, C=0.6853
1000Genomes_30x	Europe	Sub	1266	T=0.7164	A=0.0000, C=0.2836
1000Genomes_30x	South Asian	Sub	1202	T=0.7379	A=0.0000, C=0.2621
1000Genomes_30x	East Asian	Sub	1170	T=0.8137	A=0.0000, C=0.1863
1000Genomes_30x	American	Sub	980	T=0.696	A=0.002, C=0.302
1000Genomes	Global	Study-wide	5008	T=0.6328	C=0.3672
1000Genomes	African	Sub	1322	T=0.3147	C=0.6853
1000Genomes	East Asian	Sub	1008	T=0.8095	C=0.1905
1000Genomes	Europe	Sub	1006	T=0.7306	C=0.2694
1000Genomes	South Asian	Sub	978	T=0.732	C=0.268
1000Genomes	American	Sub	694	T=0.700	C=0.300
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.6679	C=0.3321
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.7945	C=0.2055
Korean Genome Project	KOREAN	Study-wide	1832	T=0.8062	C=0.1938
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.682	C=0.318
Northern Sweden	ACPOP	Study-wide	600	T=0.632	C=0.368
HapMap	Global	Study-wide	326	T=0.549	C=0.451
HapMap	American	Sub	120	T=0.658	C=0.342
HapMap	African	Sub	118	T=0.280	C=0.720
HapMap	Asian	Sub	88	T=0.76	C=0.24
SGDP_PRJ	Global	Study-wide	276	T=0.348	C=0.652
Qatari	Global	Study-wide	216	T=0.773	C=0.227
A Vietnamese Genetic Variation Database	Global	Study-wide	216	T=0.875	C=0.125
The Danish reference pan genome	Danish	Study-wide	40	T=0.65	C=0.35
Siberian	Global	Study-wide	28	T=0.43	C=0.57

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 14	NC_000014.9:g.25790383T>A
GRCh38.p14 chr 14	NC_000014.9:g.25790383T>C
GRCh38.p14 chr 14	NC_000014.9:g.25790383T>G
GRCh37.p13 chr 14	NC_000014.8:g.26259589T>A
GRCh37.p13 chr 14	NC_000014.8:g.26259589T>C
GRCh37.p13 chr 14	NC_000014.8:g.26259589T>G

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 14	NC_000014.9:g.25790383=	NC_000014.9:g.25790383T>A	NC_000014.9:g.25790383T>C	NC_000014.9:g.25790383T>G
GRCh37.p13 chr 14	NC_000014.8:g.26259589=	NC_000014.8:g.26259589T>A	NC_000014.8:g.26259589T>C	NC_000014.8:g.26259589T>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#.

64 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2855345	Jan 12, 2001 (92)
2	BCM_SSAHASNP	ss10741055	Jul 11, 2003 (116)
3	ABI	ss43672151	Mar 14, 2006 (126)
4	HGSV	ss85540778	Dec 16, 2007 (130)
5	1000GENOMES	ss108188595	Jan 23, 2009 (130)
6	1000GENOMES	ss115427804	Jan 25, 2009 (130)
7	ILLUMINA-UK	ss118385690	Feb 14, 2009 (130)
8	GMI	ss155547952	Dec 01, 2009 (131)
9	COMPLETE_GENOMICS	ss168969853	Jul 04, 2010 (132)
10	BUSHMAN	ss199844708	Jul 04, 2010 (132)
11	1000GENOMES	ss226471266	Jul 14, 2010 (132)
12	1000GENOMES	ss236469070	Jul 15, 2010 (132)
13	1000GENOMES	ss242918726	Jul 15, 2010 (132)
14	BL	ss254856323	May 09, 2011 (134)
15	GMI	ss281930335	May 04, 2012 (137)
16	GMI	ss286807705	Apr 25, 2013 (138)
17	PJP	ss291687612	May 09, 2011 (134)
18	TISHKOFF	ss563981950	Apr 25, 2013 (138)
19	SSMP	ss659642483	Apr 25, 2013 (138)
20	EVA-GONL	ss990947022	Aug 21, 2014 (142)
21	JMKIDD_LAB	ss1079504468	Aug 21, 2014 (142)
22	1000GENOMES	ss1350261097	Aug 21, 2014 (142)
23	DDI	ss1427363535	Apr 01, 2015 (144)
24	EVA_GENOME_DK	ss1577131728	Apr 01, 2015 (144)
25	EVA_DECODE	ss1694938027	Apr 01, 2015 (144)
26	HAMMER_LAB	ss1807839353	Sep 08, 2015 (146)
27	WEILL_CORNELL_DGM	ss1934323208	Feb 12, 2016 (147)
28	GENOMED	ss1967918785	Jul 19, 2016 (147)
29	JJLAB	ss2027936467	Sep 14, 2016 (149)
30	USC_VALOUEV	ss2156308497	Dec 20, 2016 (150)
31	HUMAN_LONGEVITY	ss2200444839	Dec 20, 2016 (150)
32	SYSTEMSBIOZJU	ss2628457468	Nov 08, 2017 (151)
33	GRF	ss2700723129	Nov 08, 2017 (151)
34	GNOMAD	ss2925567303	Nov 08, 2017 (151)
35	SWEGEN	ss3011897593	Nov 08, 2017 (151)
36	BIOINF_KMB_FNS_UNIBA	ss3027791361	Nov 08, 2017 (151)
37	CSHL	ss3350718629	Nov 08, 2017 (151)
38	EGCUT_WGS	ss3679137148	Jul 13, 2019 (153)
39	EVA_DECODE	ss3696311945	Jul 13, 2019 (153)
40	ACPOP	ss3740216337	Jul 13, 2019 (153)
41	EVA	ss3752098225	Jul 13, 2019 (153)
42	KHV_HUMAN_GENOMES	ss3817429787	Jul 13, 2019 (153)
43	EVA	ss3833822048	Apr 27, 2020 (154)
44	EVA	ss3840503114	Apr 27, 2020 (154)
45	EVA	ss3845990921	Apr 27, 2020 (154)
46	SGDP_PRJ	ss3881111082	Apr 27, 2020 (154)
47	KRGDB	ss3930084456	Apr 27, 2020 (154)
48	KOGIC	ss3974568436	Apr 27, 2020 (154)
49	TOPMED	ss4964159036	Apr 26, 2021 (155)
50	TOMMO_GENOMICS	ss5212392431	Apr 26, 2021 (155)
51	1000G_HIGH_COVERAGE	ss5295566470	Oct 16, 2022 (156)
52	1000G_HIGH_COVERAGE	ss5295566471	Oct 16, 2022 (156)
53	EVA	ss5414091654	Oct 16, 2022 (156)
54	HUGCELL_USP	ss5489688639	Oct 16, 2022 (156)
55	EVA	ss5511168895	Oct 16, 2022 (156)
56	1000G_HIGH_COVERAGE	ss5595499445	Oct 16, 2022 (156)
57	SANFORD_IMAGENETICS	ss5655841211	Oct 16, 2022 (156)
58	TOMMO_GENOMICS	ss5764954137	Oct 16, 2022 (156)
59	YY_MCH	ss5814589625	Oct 16, 2022 (156)
60	EVA	ss5840848186	Oct 16, 2022 (156)
61	EVA	ss5840848187	Oct 16, 2022 (156)
62	EVA	ss5850955665	Oct 16, 2022 (156)
63	EVA	ss5900597752	Oct 16, 2022 (156)
64	EVA	ss5947260343	Oct 16, 2022 (156)
65	1000Genomes	NC_000014.8 - 26259589	Oct 12, 2018 (152)
66	1000Genomes_30x	NC_000014.9 - 25790383	Oct 16, 2022 (156)
67	Genetic variation in the Estonian population	NC_000014.8 - 26259589	Oct 12, 2018 (152)
68	The Danish reference pan genome	NC_000014.8 - 26259589	Apr 27, 2020 (154)
69	gnomAD - Genomes Submission ignored due to conflicting rows: Row 445743697 (NC_000014.9:25790382:T:A 2/140130) Row 445743698 (NC_000014.9:25790382:T:C 55890/140088) Row 445743699 (NC_000014.9:25790382:T:G 1/140130)	-	Apr 26, 2021 (155)
70	gnomAD - Genomes Submission ignored due to conflicting rows: Row 445743697 (NC_000014.9:25790382:T:A 2/140130) Row 445743698 (NC_000014.9:25790382:T:C 55890/140088) Row 445743699 (NC_000014.9:25790382:T:G 1/140130)	-	Apr 26, 2021 (155)
71	gnomAD - Genomes Submission ignored due to conflicting rows: Row 445743697 (NC_000014.9:25790382:T:A 2/140130) Row 445743698 (NC_000014.9:25790382:T:C 55890/140088) Row 445743699 (NC_000014.9:25790382:T:G 1/140130)	-	Apr 26, 2021 (155)
72	Genome of the Netherlands Release 5	NC_000014.8 - 26259589	Apr 27, 2020 (154)
73	HapMap	NC_000014.9 - 25790383	Apr 27, 2020 (154)
74	KOREAN population from KRGDB	NC_000014.8 - 26259589	Apr 27, 2020 (154)
75	Korean Genome Project	NC_000014.9 - 25790383	Apr 27, 2020 (154)
76	Northern Sweden	NC_000014.8 - 26259589	Jul 13, 2019 (153)
77	Qatari	NC_000014.8 - 26259589	Apr 27, 2020 (154)
78	SGDP_PRJ	NC_000014.8 - 26259589	Apr 27, 2020 (154)
79	Siberian	NC_000014.8 - 26259589	Apr 27, 2020 (154)
80	8.3KJPN	NC_000014.8 - 26259589	Apr 26, 2021 (155)
81	14KJPN	NC_000014.9 - 25790383	Oct 16, 2022 (156)
82	TopMed	NC_000014.9 - 25790383	Apr 26, 2021 (155)
83	A Vietnamese Genetic Variation Database	NC_000014.8 - 26259589	Jul 13, 2019 (153)
84	ALFA	NC_000014.9 - 25790383	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)
rs61703665	May 27, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
83025380, 2102704741, ss5295566471, ss5595499445	NC_000014.9:25790382:T:A	NC_000014.9:25790382:T:A	(self)
ss85540778, ss108188595, ss115427804, ss118385690, ss168969853, ss199844708, ss254856323, ss281930335, ss286807705, ss291687612, ss1694938027	NC_000014.7:25329428:T:C	NC_000014.9:25790382:T:C	(self)
63212351, 24875396, 3524436, 15683494, 37261850, 13501202, 16365138, 33128062, 8824851, 70361738, 7810572, ss226471266, ss236469070, ss242918726, ss563981950, ss659642483, ss990947022, ss1079504468, ss1350261097, ss1427363535, ss1577131728, ss1807839353, ss1934323208, ss1967918785, ss2027936467, ss2156308497, ss2628457468, ss2700723129, ss2925567303, ss3011897593, ss3350718629, ss3679137148, ss3740216337, ss3752098225, ss3833822048, ss3840503114, ss3881111082, ss3930084456, ss5212392431, ss5414091654, ss5511168895, ss5655841211, ss5840848186, ss5947260343	NC_000014.8:26259588:T:C	NC_000014.9:25790382:T:C	(self)
83025380, 1107935, 30946437, 98791241, 179704695, 2102704741, ss2200444839, ss3027791361, ss3696311945, ss3817429787, ss3845990921, ss3974568436, ss4964159036, ss5295566470, ss5489688639, ss5595499445, ss5764954137, ss5814589625, ss5850955665, ss5900597752	NC_000014.9:25790382:T:C	NC_000014.9:25790382:T:C	(self)
ss10741055	NT_026437.10:6179716:T:C	NC_000014.9:25790382:T:C	(self)
ss2855345, ss43672151, ss155547952	NT_026437.12:7259588:T:C	NC_000014.9:25790382:T:C	(self)
ss5840848187	NC_000014.8:26259588:T:G	NC_000014.9:25790382:T:G
2102704741	NC_000014.9:25790382:T:G	NC_000014.9:25790382: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 rs1959785

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

rs1959785