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dbSNP Short Genetic Variations

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.

rs710900

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr16:1445242 (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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.089331 (23645/264690, TOPMED)
T=0.093007 (13029/140086, GnomAD)
T=0.08871 (2506/28248, 14KJPN) (+ 13 more)
T=0.10043 (2610/25988, ALFA)
T=0.08866 (1485/16750, 8.3KJPN)
T=0.0784 (502/6404, 1000G_30x)
T=0.0811 (406/5008, 1000G)
T=0.0893 (400/4480, Estonian)
T=0.1100 (424/3854, ALSPAC)
T=0.1149 (426/3708, TWINSUK)
T=0.0862 (252/2924, KOREAN)
T=0.117 (70/600, NorthernSweden)
T=0.066 (36/548, SGDP_PRJ)
T=0.093 (20/216, Qatari)
T=0.09 (5/54, Siberian)
T=0.23 (9/40, GENOME_DK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CLCN7 : 3 Prime UTR Variant
CCDC154 : 2KB Upstream 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 25988 T=0.10043 G=0.89957
European Sub 18662 T=0.10604 G=0.89396
African Sub 5580 T=0.0903 G=0.9097
African Others Sub 198 T=0.061 G=0.939
African American Sub 5382 T=0.0914 G=0.9086
Asian Sub 112 T=0.018 G=0.982
East Asian Sub 86 T=0.02 G=0.98
Other Asian Sub 26 T=0.00 G=1.00
Latin American 1 Sub 146 T=0.096 G=0.904
Latin American 2 Sub 610 T=0.051 G=0.949
South Asian Sub 98 T=0.15 G=0.85
Other Sub 780 T=0.083 G=0.917


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 T=0.089331 G=0.910669
gnomAD - Genomes Global Study-wide 140086 T=0.093007 G=0.906993
gnomAD - Genomes European Sub 75844 T=0.10700 G=0.89300
gnomAD - Genomes African Sub 41970 T=0.08673 G=0.91327
gnomAD - Genomes American Sub 13666 T=0.05525 G=0.94475
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.0557 G=0.9443
gnomAD - Genomes East Asian Sub 3132 T=0.0498 G=0.9502
gnomAD - Genomes Other Sub 2150 T=0.0828 G=0.9172
14KJPN JAPANESE Study-wide 28248 T=0.08871 G=0.91129
Allele Frequency Aggregator Total Global 25988 T=0.10043 G=0.89957
Allele Frequency Aggregator European Sub 18662 T=0.10604 G=0.89396
Allele Frequency Aggregator African Sub 5580 T=0.0903 G=0.9097
Allele Frequency Aggregator Other Sub 780 T=0.083 G=0.917
Allele Frequency Aggregator Latin American 2 Sub 610 T=0.051 G=0.949
Allele Frequency Aggregator Latin American 1 Sub 146 T=0.096 G=0.904
Allele Frequency Aggregator Asian Sub 112 T=0.018 G=0.982
Allele Frequency Aggregator South Asian Sub 98 T=0.15 G=0.85
8.3KJPN JAPANESE Study-wide 16750 T=0.08866 G=0.91134
1000Genomes_30x Global Study-wide 6404 T=0.0784 G=0.9216
1000Genomes_30x African Sub 1786 T=0.0829 G=0.9171
1000Genomes_30x Europe Sub 1266 T=0.0972 G=0.9028
1000Genomes_30x South Asian Sub 1202 T=0.1073 G=0.8927
1000Genomes_30x East Asian Sub 1170 T=0.0479 G=0.9521
1000Genomes_30x American Sub 980 T=0.047 G=0.953
1000Genomes Global Study-wide 5008 T=0.0811 G=0.9189
1000Genomes African Sub 1322 T=0.0938 G=0.9062
1000Genomes East Asian Sub 1008 T=0.0446 G=0.9554
1000Genomes Europe Sub 1006 T=0.0885 G=0.9115
1000Genomes South Asian Sub 978 T=0.113 G=0.887
1000Genomes American Sub 694 T=0.053 G=0.947
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.0893 G=0.9107
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.1100 G=0.8900
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.1149 G=0.8851
KOREAN population from KRGDB KOREAN Study-wide 2924 T=0.0862 A=0.0000, G=0.9138
Northern Sweden ACPOP Study-wide 600 T=0.117 G=0.883
SGDP_PRJ Global Study-wide 548 T=0.066 G=0.934
Qatari Global Study-wide 216 T=0.093 G=0.907
Siberian Global Study-wide 54 T=0.09 G=0.91
The Danish reference pan genome Danish Study-wide 40 T=0.23 G=0.78
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.1445242T>A
GRCh38.p14 chr 16 NC_000016.10:g.1445242T>G
GRCh37.p13 chr 16 NC_000016.9:g.1495243T>A
GRCh37.p13 chr 16 NC_000016.9:g.1495243T>G
CLCN7 RefSeqGene NG_007567.1:g.34843A>T
CLCN7 RefSeqGene NG_007567.1:g.34843A>C
Gene: CLCN7, chloride voltage-gated channel 7 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CLCN7 transcript variant 1 NM_001287.6:c.*1389= N/A 3 Prime UTR Variant
CLCN7 transcript variant 2 NM_001114331.3:c.*1389= N/A 3 Prime UTR Variant
CLCN7 transcript variant X1 XM_011522354.2:c.*1389= N/A 3 Prime UTR Variant
Gene: CCDC154, coiled-coil domain containing 154 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
CCDC154 transcript NM_001143980.3:c. N/A Upstream Transcript 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.

Allele: G (allele ID: 333780 )
ClinVar Accession Disease Names Clinical Significance
RCV000396092.3 Osteopetrosis Benign
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 T= A G
GRCh38.p14 chr 16 NC_000016.10:g.1445242= NC_000016.10:g.1445242T>A NC_000016.10:g.1445242T>G
GRCh37.p13 chr 16 NC_000016.9:g.1495243= NC_000016.9:g.1495243T>A NC_000016.9:g.1495243T>G
CLCN7 RefSeqGene NG_007567.1:g.34843= NG_007567.1:g.34843A>T NG_007567.1:g.34843A>C
CLCN7 transcript variant 1 NM_001287.6:c.*1389= NM_001287.6:c.*1389A>T NM_001287.6:c.*1389A>C
CLCN7 transcript variant 1 NM_001287.5:c.*1389= NM_001287.5:c.*1389A>T NM_001287.5:c.*1389A>C
CLCN7 transcript variant 2 NM_001114331.3:c.*1389= NM_001114331.3:c.*1389A>T NM_001114331.3:c.*1389A>C
CLCN7 transcript variant 2 NM_001114331.2:c.*1389= NM_001114331.2:c.*1389A>T NM_001114331.2:c.*1389A>C
CLCN7 transcript variant X1 XM_011522354.2:c.*1389= XM_011522354.2:c.*1389A>T XM_011522354.2:c.*1389A>C
CLCN7 transcript variant X1 XM_011522354.1:c.*1389= XM_011522354.1:c.*1389A>T XM_011522354.1:c.*1389A>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#.

84 SubSNP, 16 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss1382247 Oct 04, 2000 (86)
2 LEE ss1525189 Oct 04, 2000 (86)
3 LEE ss4415883 May 29, 2002 (106)
4 WI_SSAHASNP ss12352685 Jul 11, 2003 (116)
5 CGAP-GAI ss16267069 Feb 27, 2004 (120)
6 SSAHASNP ss21313058 Apr 05, 2004 (121)
7 ABI ss43927220 Mar 13, 2006 (126)
8 HGSV ss81025354 Dec 15, 2007 (130)
9 BCMHGSC_JDW ss90287218 Mar 24, 2008 (129)
10 HUMANGENOME_JCVI ss96617713 Feb 05, 2009 (130)
11 BGI ss106453742 Feb 05, 2009 (130)
12 ILLUMINA-UK ss118154342 Feb 14, 2009 (130)
13 ENSEMBL ss136543044 Dec 01, 2009 (131)
14 ENSEMBL ss136789478 Dec 01, 2009 (131)
15 GMI ss156978247 Dec 01, 2009 (131)
16 COMPLETE_GENOMICS ss167635736 Jul 04, 2010 (132)
17 COMPLETE_GENOMICS ss168861964 Jul 04, 2010 (132)
18 BUSHMAN ss201316957 Jul 04, 2010 (132)
19 BCM-HGSC-SUB ss207697907 Jul 04, 2010 (132)
20 1000GENOMES ss210887881 Jul 14, 2010 (132)
21 1000GENOMES ss227093055 Jul 14, 2010 (132)
22 1000GENOMES ss236918452 Jul 15, 2010 (132)
23 1000GENOMES ss243279561 Jul 15, 2010 (132)
24 GMI ss282403496 May 04, 2012 (137)
25 GMI ss287018562 Apr 25, 2013 (138)
26 PJP ss291833309 May 09, 2011 (134)
27 ILLUMINA ss483324836 May 04, 2012 (137)
28 ILLUMINA ss483483406 May 04, 2012 (137)
29 TISHKOFF ss564718572 Apr 25, 2013 (138)
30 SSMP ss660465827 Apr 25, 2013 (138)
31 ILLUMINA ss782105536 Sep 08, 2015 (146)
32 EVA-GONL ss992188100 Aug 21, 2014 (142)
33 JMKIDD_LAB ss1080416157 Aug 21, 2014 (142)
34 1000GENOMES ss1355011218 Aug 21, 2014 (142)
35 DDI ss1427749518 Apr 01, 2015 (144)
36 EVA_GENOME_DK ss1577796147 Apr 01, 2015 (144)
37 EVA_UK10K_ALSPAC ss1633816772 Apr 01, 2015 (144)
38 EVA_UK10K_TWINSUK ss1676810805 Apr 01, 2015 (144)
39 EVA_DECODE ss1696220182 Apr 01, 2015 (144)
40 HAMMER_LAB ss1808377435 Sep 08, 2015 (146)
41 WEILL_CORNELL_DGM ss1935595710 Feb 12, 2016 (147)
42 GENOMED ss1968198553 Jul 19, 2016 (147)
43 JJLAB ss2028584101 Sep 14, 2016 (149)
44 USC_VALOUEV ss2156993645 Nov 08, 2017 (151)
45 HUMAN_LONGEVITY ss2209885421 Dec 20, 2016 (150)
46 SYSTEMSBIOZJU ss2628786262 Nov 08, 2017 (151)
47 ILLUMINA ss2633282432 Nov 08, 2017 (151)
48 GRF ss2701487279 Nov 08, 2017 (151)
49 GNOMAD ss2939294863 Nov 08, 2017 (151)
50 AFFY ss2985695375 Nov 08, 2017 (151)
51 SWEGEN ss3013918426 Nov 08, 2017 (151)
52 BIOINF_KMB_FNS_UNIBA ss3028116391 Nov 08, 2017 (151)
53 CSHL ss3351292855 Nov 08, 2017 (151)
54 ILLUMINA ss3641938777 Oct 12, 2018 (152)
55 OMUKHERJEE_ADBS ss3646484130 Oct 12, 2018 (152)
56 URBANLAB ss3650443310 Oct 12, 2018 (152)
57 EGCUT_WGS ss3681044528 Jul 13, 2019 (153)
58 EVA_DECODE ss3698660584 Jul 13, 2019 (153)
59 ACPOP ss3741258718 Jul 13, 2019 (153)
60 EVA ss3753570757 Jul 13, 2019 (153)
61 PACBIO ss3787956248 Jul 13, 2019 (153)
62 PACBIO ss3792952216 Jul 13, 2019 (153)
63 PACBIO ss3797837099 Jul 13, 2019 (153)
64 KHV_HUMAN_GENOMES ss3818872298 Jul 13, 2019 (153)
65 EVA ss3834428711 Apr 27, 2020 (154)
66 EVA ss3840818909 Apr 27, 2020 (154)
67 EVA ss3846309554 Apr 27, 2020 (154)
68 SGDP_PRJ ss3883746310 Apr 27, 2020 (154)
69 KRGDB ss3933019155 Apr 27, 2020 (154)
70 FSA-LAB ss3984084227 Apr 26, 2021 (155)
71 EVA ss3986069177 Apr 26, 2021 (155)
72 TOPMED ss5004701529 Apr 26, 2021 (155)
73 TOMMO_GENOMICS ss5218003668 Apr 26, 2021 (155)
74 1000G_HIGH_COVERAGE ss5299810357 Oct 16, 2022 (156)
75 EVA ss5421730905 Oct 16, 2022 (156)
76 HUGCELL_USP ss5493376283 Oct 16, 2022 (156)
77 1000G_HIGH_COVERAGE ss5601883652 Oct 16, 2022 (156)
78 SANFORD_IMAGENETICS ss5658283339 Oct 16, 2022 (156)
79 TOMMO_GENOMICS ss5772355706 Oct 16, 2022 (156)
80 YY_MCH ss5815679662 Oct 16, 2022 (156)
81 EVA ss5845978945 Oct 16, 2022 (156)
82 EVA ss5851453098 Oct 16, 2022 (156)
83 EVA ss5897919422 Oct 16, 2022 (156)
84 EVA ss5949708142 Oct 16, 2022 (156)
85 1000Genomes NC_000016.9 - 1495243 Oct 12, 2018 (152)
86 1000Genomes_30x NC_000016.10 - 1445242 Oct 16, 2022 (156)
87 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 1495243 Oct 12, 2018 (152)
88 Genetic variation in the Estonian population NC_000016.9 - 1495243 Oct 12, 2018 (152)
89 The Danish reference pan genome NC_000016.9 - 1495243 Apr 27, 2020 (154)
90 gnomAD - Genomes NC_000016.10 - 1445242 Apr 26, 2021 (155)
91 KOREAN population from KRGDB NC_000016.9 - 1495243 Apr 27, 2020 (154)
92 Northern Sweden NC_000016.9 - 1495243 Jul 13, 2019 (153)
93 Qatari NC_000016.9 - 1495243 Apr 27, 2020 (154)
94 SGDP_PRJ NC_000016.9 - 1495243 Apr 27, 2020 (154)
95 Siberian NC_000016.9 - 1495243 Apr 27, 2020 (154)
96 8.3KJPN NC_000016.9 - 1495243 Apr 26, 2021 (155)
97 14KJPN NC_000016.10 - 1445242 Oct 16, 2022 (156)
98 TopMed NC_000016.10 - 1445242 Apr 26, 2021 (155)
99 UK 10K study - Twins NC_000016.9 - 1495243 Oct 12, 2018 (152)
100 ALFA NC_000016.10 - 1445242 Apr 26, 2021 (155)
101 ClinVar RCV000396092.3 Oct 16, 2022 (156)
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)
rs3190821 Jul 03, 2002 (106)
rs58541840 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
40196549, ss3933019155 NC_000016.9:1495242:T:A NC_000016.10:1445241:T:A (self)
ss81025354, ss90287218, ss118154342, ss167635736, ss168861964, ss201316957, ss207697907, ss210887881, ss282403496, ss287018562, ss291833309, ss483483406, ss1696220182 NC_000016.8:1435243:T:G NC_000016.10:1445241:T:G (self)
68137368, 37836182, 26782776, 4013337, 40196549, 14543583, 17637632, 35763290, 9509999, 75972975, 37836182, ss227093055, ss236918452, ss243279561, ss483324836, ss564718572, ss660465827, ss782105536, ss992188100, ss1080416157, ss1355011218, ss1427749518, ss1577796147, ss1633816772, ss1676810805, ss1808377435, ss1935595710, ss1968198553, ss2028584101, ss2156993645, ss2628786262, ss2633282432, ss2701487279, ss2939294863, ss2985695375, ss3013918426, ss3351292855, ss3641938777, ss3646484130, ss3681044528, ss3741258718, ss3753570757, ss3787956248, ss3792952216, ss3797837099, ss3834428711, ss3840818909, ss3883746310, ss3933019155, ss3984084227, ss3986069177, ss5218003668, ss5421730905, ss5658283339, ss5845978945, ss5949708142 NC_000016.9:1495242:T:G NC_000016.10:1445241:T:G (self)
RCV000396092.3, 89409587, 480231897, 106192810, 220247190, 12316582916, ss2209885421, ss3028116391, ss3650443310, ss3698660584, ss3818872298, ss3846309554, ss5004701529, ss5299810357, ss5493376283, ss5601883652, ss5772355706, ss5815679662, ss5851453098, ss5897919422 NC_000016.10:1445241:T:G NC_000016.10:1445241:T:G (self)
ss1382247, ss1525189, ss4415883, ss16267069, ss43927220, ss96617713, ss106453742, ss136543044, ss136789478, ss156978247 NT_010393.16:1435242:T:G NC_000016.10:1445241:T:G (self)
ss12352685, ss21313058 NT_037887.3:1435243:T:G NC_000016.10:1445241:T:G (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 rs710900

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