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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs244414

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr16:69612875 (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>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.107435 (28437/264690, TOPMED)
G=0.111504 (15409/138192, GnomAD)
G=0.16130 (4558/28258, 14KJPN) (+ 11 more)
G=0.12973 (2229/17182, ALFA)
G=0.16106 (2699/16758, 8.3KJPN)
G=0.0912 (584/6404, 1000G_30x)
G=0.0915 (458/5008, 1000G)
G=0.1464 (633/4324, Estonian)
G=0.1508 (581/3854, ALSPAC)
G=0.1597 (592/3708, TWINSUK)
G=0.071 (39/552, SGDP_PRJ)
G=0.111 (24/216, Qatari)
G=0.25 (10/40, GENOME_DK)
G=0.17 (7/40, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NFAT5 : 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 17182 G=0.12973 A=0.87027, C=0.00000
European Sub 13340 G=0.14655 A=0.85345, C=0.00000
African Sub 2376 G=0.0366 A=0.9634, C=0.0000
African Others Sub 90 G=0.02 A=0.98, C=0.00
African American Sub 2286 G=0.0372 A=0.9628, C=0.0000
Asian Sub 112 G=0.089 A=0.911, C=0.000
East Asian Sub 86 G=0.09 A=0.91, C=0.00
Other Asian Sub 26 G=0.08 A=0.92, C=0.00
Latin American 1 Sub 146 G=0.082 A=0.918, C=0.000
Latin American 2 Sub 610 G=0.161 A=0.839, C=0.000
South Asian Sub 98 G=0.16 A=0.84, C=0.00
Other Sub 500 G=0.102 A=0.898, C=0.000


Help

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 G=0.107435 A=0.892565
gnomAD - Genomes Global Study-wide 138192 G=0.111504 A=0.888496
gnomAD - Genomes European Sub 74616 G=0.14879 A=0.85121
gnomAD - Genomes African Sub 41540 G=0.04292 A=0.95708
gnomAD - Genomes American Sub 13490 G=0.13091 A=0.86909
gnomAD - Genomes Ashkenazi Jewish Sub 3312 G=0.0942 A=0.9058
gnomAD - Genomes East Asian Sub 3118 G=0.0571 A=0.9429
gnomAD - Genomes Other Sub 2116 G=0.1267 A=0.8733
14KJPN JAPANESE Study-wide 28258 G=0.16130 A=0.83870
Allele Frequency Aggregator Total Global 17182 G=0.12973 A=0.87027, C=0.00000
Allele Frequency Aggregator European Sub 13340 G=0.14655 A=0.85345, C=0.00000
Allele Frequency Aggregator African Sub 2376 G=0.0366 A=0.9634, C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.161 A=0.839, C=0.000
Allele Frequency Aggregator Other Sub 500 G=0.102 A=0.898, C=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.082 A=0.918, C=0.000
Allele Frequency Aggregator Asian Sub 112 G=0.089 A=0.911, C=0.000
Allele Frequency Aggregator South Asian Sub 98 G=0.16 A=0.84, C=0.00
8.3KJPN JAPANESE Study-wide 16758 G=0.16106 A=0.83894
1000Genomes_30x Global Study-wide 6404 G=0.0912 A=0.9088
1000Genomes_30x African Sub 1786 G=0.0157 A=0.9843
1000Genomes_30x Europe Sub 1266 G=0.1493 A=0.8507
1000Genomes_30x South Asian Sub 1202 G=0.1298 A=0.8702
1000Genomes_30x East Asian Sub 1170 G=0.0795 A=0.9205
1000Genomes_30x American Sub 980 G=0.120 A=0.880
1000Genomes Global Study-wide 5008 G=0.0915 A=0.9085
1000Genomes African Sub 1322 G=0.0182 A=0.9818
1000Genomes East Asian Sub 1008 G=0.0774 A=0.9226
1000Genomes Europe Sub 1006 G=0.1421 A=0.8579
1000Genomes South Asian Sub 978 G=0.129 A=0.871
1000Genomes American Sub 694 G=0.125 A=0.875
Genetic variation in the Estonian population Estonian Study-wide 4324 G=0.1464 A=0.8536
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.1508 A=0.8492
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.1597 A=0.8403
SGDP_PRJ Global Study-wide 552 G=0.071 A=0.929
Qatari Global Study-wide 216 G=0.111 A=0.889
The Danish reference pan genome Danish Study-wide 40 G=0.25 A=0.75
Siberian Global Study-wide 40 G=0.17 A=0.82
Help

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 16 NC_000016.10:g.69612875G>A
GRCh38.p14 chr 16 NC_000016.10:g.69612875G>C
GRCh37.p13 chr 16 NC_000016.9:g.69646778G>A
GRCh37.p13 chr 16 NC_000016.9:g.69646778G>C
NFAT5 RefSeqGene (LRG_1332) NG_029600.1:g.52782G>A
NFAT5 RefSeqGene (LRG_1332) NG_029600.1:g.52782G>C
Gene: NFAT5, nuclear factor of activated T cells 5 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
NFAT5 transcript variant 6 NM_001113178.3:c.128-1352…

NM_001113178.3:c.128-13528G>A

 		N/A Intron Variant
NFAT5 transcript variant 7 NM_001367709.1:c.-126-135…

NM_001367709.1:c.-126-13528G>A

 		N/A Intron Variant
NFAT5 transcript variant 3 NM_006599.4:c.74-13528G>A N/A Intron Variant
NFAT5 transcript variant 2 NM_138713.4:c.128-13528G>A N/A Intron Variant
NFAT5 transcript variant 1 NM_138714.4:c.-217-13528G…

NM_138714.4:c.-217-13528G>A

 		N/A Intron Variant
NFAT5 transcript variant 4 NM_173214.3:c.-217-13528G…

NM_173214.3:c.-217-13528G>A

 		N/A Intron Variant
NFAT5 transcript variant 5 NM_173215.3:c.-217-13528G…

NM_173215.3:c.-217-13528G>A

 		N/A Intron Variant
NFAT5 transcript variant X1 XM_011522817.4:c.74-13528…

XM_011522817.4:c.74-13528G>A

 		N/A Intron Variant
NFAT5 transcript variant X8 XM_011522820.4:c. N/A Genic Upstream Transcript Variant
NFAT5 transcript variant X10 XM_011522822.4:c. N/A Genic Upstream Transcript Variant
NFAT5 transcript variant X9 XM_017022872.3:c. N/A Genic Upstream Transcript Variant
NFAT5 transcript variant X2 XM_047433510.1:c. N/A Genic Upstream Transcript Variant
NFAT5 transcript variant X3 XM_047433511.1:c. N/A Genic Upstream Transcript Variant
NFAT5 transcript variant X5 XM_047433512.1:c. N/A Genic Upstream Transcript Variant
NFAT5 transcript variant X6 XM_047433513.1:c. N/A Genic Upstream Transcript Variant
NFAT5 transcript variant X7 XM_047433514.1:c. N/A Genic Upstream Transcript Variant
NFAT5 transcript variant X11 XM_047433515.1:c. N/A Genic Upstream Transcript Variant
NFAT5 transcript variant X4 XR_007064848.1:n. N/A Intron Variant
Help

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
Help

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= A C
GRCh38.p14 chr 16 NC_000016.10:g.69612875= NC_000016.10:g.69612875G>A NC_000016.10:g.69612875G>C
GRCh37.p13 chr 16 NC_000016.9:g.69646778= NC_000016.9:g.69646778G>A NC_000016.9:g.69646778G>C
NFAT5 RefSeqGene (LRG_1332) NG_029600.1:g.52782= NG_029600.1:g.52782G>A NG_029600.1:g.52782G>C
NFAT5 transcript variant 6 NM_001113178.2:c.128-13528= NM_001113178.2:c.128-13528G>A NM_001113178.2:c.128-13528G>C
NFAT5 transcript variant 6 NM_001113178.3:c.128-13528= NM_001113178.3:c.128-13528G>A NM_001113178.3:c.128-13528G>C
NFAT5 transcript variant 7 NM_001367709.1:c.-126-13528= NM_001367709.1:c.-126-13528G>A NM_001367709.1:c.-126-13528G>C
NFAT5 transcript variant 3 NM_006599.3:c.74-13528= NM_006599.3:c.74-13528G>A NM_006599.3:c.74-13528G>C
NFAT5 transcript variant 3 NM_006599.4:c.74-13528= NM_006599.4:c.74-13528G>A NM_006599.4:c.74-13528G>C
NFAT5 transcript variant 2 NM_138713.3:c.128-13528= NM_138713.3:c.128-13528G>A NM_138713.3:c.128-13528G>C
NFAT5 transcript variant 2 NM_138713.4:c.128-13528= NM_138713.4:c.128-13528G>A NM_138713.4:c.128-13528G>C
NFAT5 transcript variant 1 NM_138714.3:c.-217-13528= NM_138714.3:c.-217-13528G>A NM_138714.3:c.-217-13528G>C
NFAT5 transcript variant 1 NM_138714.4:c.-217-13528= NM_138714.4:c.-217-13528G>A NM_138714.4:c.-217-13528G>C
NFAT5 transcript variant 4 NM_173214.2:c.-217-13528= NM_173214.2:c.-217-13528G>A NM_173214.2:c.-217-13528G>C
NFAT5 transcript variant 4 NM_173214.3:c.-217-13528= NM_173214.3:c.-217-13528G>A NM_173214.3:c.-217-13528G>C
NFAT5 transcript variant 5 NM_173215.2:c.-217-13528= NM_173215.2:c.-217-13528G>A NM_173215.2:c.-217-13528G>C
NFAT5 transcript variant 5 NM_173215.3:c.-217-13528= NM_173215.3:c.-217-13528G>A NM_173215.3:c.-217-13528G>C
NFAT5 transcript variant X1 XM_011522817.4:c.74-13528= XM_011522817.4:c.74-13528G>A XM_011522817.4:c.74-13528G>C
Help

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#.

67 SubSNP, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss314169 Jul 12, 2000 (79)
2 SC_JCM ss607711 Jul 16, 2000 (87)
3 KWOK ss1120456 Oct 04, 2000 (86)
4 KWOK ss1605806 Oct 18, 2000 (87)
5 TSC-CSHL ss2148336 Oct 08, 2002 (108)
6 SC_JCM ss3618288 Sep 28, 2001 (100)
7 TSC-CSHL ss5445877 Oct 08, 2002 (108)
8 SC_JCM ss6203704 Feb 20, 2003 (111)
9 WI_SSAHASNP ss6600753 Feb 20, 2003 (111)
10 WI_SSAHASNP ss12366188 Jul 11, 2003 (116)
11 CSHL-HAPMAP ss19337149 Feb 27, 2004 (120)
12 SSAHASNP ss21326434 Apr 05, 2004 (121)
13 HGSV ss78475144 Dec 07, 2007 (129)
14 HUMANGENOME_JCVI ss96644108 Feb 05, 2009 (130)
15 BGI ss106478780 Feb 05, 2009 (130)
16 1000GENOMES ss109412702 Jan 24, 2009 (130)
17 ILLUMINA-UK ss118293243 Dec 01, 2009 (131)
18 ENSEMBL ss136700375 Dec 01, 2009 (131)
19 GMI ss157484233 Dec 01, 2009 (131)
20 BCM-HGSC-SUB ss207717904 Jul 04, 2010 (132)
21 1000GENOMES ss211728857 Jul 14, 2010 (132)
22 1000GENOMES ss227305245 Jul 14, 2010 (132)
23 1000GENOMES ss237070601 Jul 15, 2010 (132)
24 1000GENOMES ss243401068 Jul 15, 2010 (132)
25 BL ss255783101 May 09, 2011 (134)
26 GMI ss282577548 May 04, 2012 (137)
27 GMI ss287093438 Apr 25, 2013 (138)
28 PJP ss291864566 May 09, 2011 (134)
29 1000GENOMES ss1356739000 Aug 21, 2014 (142)
30 DDI ss1427882897 Apr 01, 2015 (144)
31 EVA_GENOME_DK ss1577964641 Apr 01, 2015 (144)
32 EVA_UK10K_ALSPAC ss1634687617 Apr 01, 2015 (144)
33 EVA_UK10K_TWINSUK ss1677681650 Apr 01, 2015 (144)
34 HAMMER_LAB ss1808566148 Sep 08, 2015 (146)
35 WEILL_CORNELL_DGM ss1936047796 Feb 12, 2016 (147)
36 JJLAB ss2028809722 Sep 14, 2016 (149)
37 USC_VALOUEV ss2157248853 Dec 20, 2016 (150)
38 SYSTEMSBIOZJU ss2628894778 Nov 08, 2017 (151)
39 GRF ss2701777023 Nov 08, 2017 (151)
40 GNOMAD ss2944434748 Nov 08, 2017 (151)
41 SWEGEN ss3014715037 Nov 08, 2017 (151)
42 BIOINF_KMB_FNS_UNIBA ss3028222248 Nov 08, 2017 (151)
43 URBANLAB ss3650534390 Oct 12, 2018 (152)
44 URBANLAB ss3650534391 Oct 12, 2018 (152)
45 EGCUT_WGS ss3681698529 Jul 13, 2019 (153)
46 EVA_DECODE ss3699511076 Jul 13, 2019 (153)
47 EVA ss3754087697 Jul 13, 2019 (153)
48 PACBIO ss3788072262 Jul 13, 2019 (153)
49 PACBIO ss3793049061 Jul 13, 2019 (153)
50 PACBIO ss3797934127 Jul 13, 2019 (153)
51 KHV_HUMAN_GENOMES ss3819369482 Jul 13, 2019 (153)
52 EVA ss3834630768 Apr 27, 2020 (154)
53 EVA ss3840920527 Apr 27, 2020 (154)
54 EVA ss3846412894 Apr 27, 2020 (154)
55 SGDP_PRJ ss3884696235 Apr 27, 2020 (154)
56 TOPMED ss5019785788 Apr 26, 2021 (155)
57 TOMMO_GENOMICS ss5220147608 Apr 26, 2021 (155)
58 1000G_HIGH_COVERAGE ss5301393085 Oct 17, 2022 (156)
59 HUGCELL_USP ss5494704072 Oct 17, 2022 (156)
60 EVA ss5511650059 Oct 17, 2022 (156)
61 1000G_HIGH_COVERAGE ss5604271250 Oct 17, 2022 (156)
62 SANFORD_IMAGENETICS ss5659144493 Oct 17, 2022 (156)
63 TOMMO_GENOMICS ss5775325399 Oct 17, 2022 (156)
64 YY_MCH ss5816078003 Oct 17, 2022 (156)
65 EVA ss5851616790 Oct 17, 2022 (156)
66 EVA ss5899596673 Oct 17, 2022 (156)
67 EVA ss5950546878 Oct 17, 2022 (156)
68 1000Genomes NC_000016.9 - 69646778 Oct 12, 2018 (152)
69 1000Genomes_30x NC_000016.10 - 69612875 Oct 17, 2022 (156)
70 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 69646778 Oct 12, 2018 (152)
71 Genetic variation in the Estonian population NC_000016.9 - 69646778 Oct 12, 2018 (152)
72 The Danish reference pan genome NC_000016.9 - 69646778 Apr 27, 2020 (154)
73 gnomAD - Genomes NC_000016.10 - 69612875 Apr 26, 2021 (155)
74 Qatari NC_000016.9 - 69646778 Apr 27, 2020 (154)
75 SGDP_PRJ NC_000016.9 - 69646778 Apr 27, 2020 (154)
76 Siberian NC_000016.9 - 69646778 Apr 27, 2020 (154)
77 8.3KJPN NC_000016.9 - 69646778 Apr 26, 2021 (155)
78 14KJPN NC_000016.10 - 69612875 Oct 17, 2022 (156)
79 TopMed NC_000016.10 - 69612875 Apr 26, 2021 (155)
80 UK 10K study - Twins NC_000016.9 - 69646778 Oct 12, 2018 (152)
81 ALFA NC_000016.10 - 69612875 Apr 26, 2021 (155)
Help

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)
rs452544 Oct 23, 2000 (87)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78475144, ss109412702, ss118293243, ss207717904, ss211728857, ss255783101, ss282577548, ss287093438, ss291864566 NC_000016.8:68204278:G:A NC_000016.10:69612874:G:A (self)
69919550, 38790616, 27436777, 4174939, 18089718, 36713215, 9765207, 78116915, 38790616, ss227305245, ss237070601, ss243401068, ss1356739000, ss1427882897, ss1577964641, ss1634687617, ss1677681650, ss1808566148, ss1936047796, ss2028809722, ss2157248853, ss2628894778, ss2701777023, ss2944434748, ss3014715037, ss3681698529, ss3754087697, ss3788072262, ss3793049061, ss3797934127, ss3834630768, ss3840920527, ss3884696235, ss5220147608, ss5511650059, ss5659144493, ss5950546878 NC_000016.9:69646777:G:A NC_000016.10:69612874:G:A (self)
91797185, 493239023, 109162503, 235331449, 11420765055, ss3028222248, ss3650534390, ss3650534391, ss3699511076, ss3819369482, ss3846412894, ss5019785788, ss5301393085, ss5494704072, ss5604271250, ss5775325399, ss5816078003, ss5851616790, ss5899596673 NC_000016.10:69612874:G:A NC_000016.10:69612874:G:A (self)
ss12366188 NT_010498.13:18368286:G:A NC_000016.10:69612874:G:A (self)
ss19337149, ss21326434 NT_010498.14:18368281:G:A NC_000016.10:69612874:G:A (self)
ss314169, ss607711, ss1120456, ss1605806, ss2148336, ss3618288, ss5445877, ss6203704, ss6600753, ss96644108, ss106478780, ss136700375, ss157484233 NT_010498.15:23260976:G:A NC_000016.10:69612874:G:A (self)
11420765055 NC_000016.10:69612874:G:C NC_000016.10:69612874:G:C (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs244414

Help

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.

Software version is: 2.0.1.post761+d5e8e07