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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 Aliases 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.

rs250585

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr16:23389755 (GRCh38.p12) 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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.2062 (6459/31326, GnomAD)
T=0.223 (1115/5008, 1000G)
T=0.231 (1037/4480, Estonian) (+ 2 more)
T=0.12 (73/600, NorthernSweden)
T=0.24 (50/210, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
COG7 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
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.p12 chr 16 NC_000016.10:g.23389755C>T
GRCh37.p13 chr 16 NC_000016.9:g.23401076C>T
COG7 RefSeqGene NG_021287.1:g.68437G>A
Gene: COG7, component of oligomeric golgi complex 7 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
COG7 transcript NM_153603.4:c. N/A Intron Variant
COG7 transcript variant X3 XM_017023870.1:c. N/A Intron Variant
COG7 transcript variant X1 XR_002957852.1:n. N/A Intron Variant
COG7 transcript variant X2 XR_429680.2: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

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
gnomAD - Genomes Global Study-wide 31326 C=0.7938 T=0.2062
gnomAD - Genomes European Sub 18858 C=0.8006 T=0.1994
gnomAD - Genomes African Sub 8690 C=0.785 T=0.215
gnomAD - Genomes East Asian Sub 1556 C=0.712 T=0.288
gnomAD - Genomes Other Sub 1086 C=0.802 T=0.198
gnomAD - Genomes American Sub 848 C=0.85 T=0.15
gnomAD - Genomes Ashkenazi Jewish Sub 288 C=0.88 T=0.12
1000Genomes Global Study-wide 5008 C=0.777 T=0.223
1000Genomes African Sub 1322 C=0.752 T=0.248
1000Genomes East Asian Sub 1008 C=0.726 T=0.274
1000Genomes Europe Sub 1006 C=0.831 T=0.169
1000Genomes South Asian Sub 978 C=0.76 T=0.24
1000Genomes American Sub 694 C=0.85 T=0.15
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.769 T=0.231
Northern Sweden ACPOP Study-wide 600 C=0.88 T=0.12
A Vietnamese Genetic Variation Database Global Study-wide 210 C=0.76 T=0.24
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 C= T Note
GRCh38.p12 chr 16 NC_000016.10:g.23389755= NC_000016.10:g.23389755C>T
GRCh37.p13 chr 16 NC_000016.9:g.23401076= NC_000016.9:g.23401076C>T
COG7 RefSeqGene NG_021287.1:g.68437= NG_021287.1:g.68437G>A
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, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss324670 Jul 12, 2000 (79)
2 SC_JCM ss588264 Jul 16, 2000 (86)
3 SC_JCM ss646924 Aug 11, 2000 (86)
4 KWOK ss891023 Oct 04, 2000 (86)
5 SC_JCM ss3721900 Sep 28, 2001 (100)
6 PERLEGEN ss23964723 Sep 20, 2004 (123)
7 PERLEGEN ss69341600 May 18, 2007 (127)
8 AFFY ss74826547 Aug 16, 2007 (128)
9 AFFY ss76536853 Dec 07, 2007 (129)
10 BCMHGSC_JDW ss90348376 Mar 24, 2008 (129)
11 HUMANGENOME_JCVI ss96674760 Feb 06, 2009 (130)
12 BGI ss103286492 Dec 01, 2009 (131)
13 KRIBB_YJKIM ss104812637 Feb 06, 2009 (130)
14 ILLUMINA-UK ss118220584 Feb 14, 2009 (130)
15 ENSEMBL ss136633509 Dec 01, 2009 (131)
16 ENSEMBL ss142853613 Dec 01, 2009 (131)
17 GMI ss157197686 Dec 01, 2009 (131)
18 ILLUMINA ss160553877 Dec 01, 2009 (131)
19 COMPLETE_GENOMICS ss168020587 Jul 04, 2010 (132)
20 BUSHMAN ss201553332 Jul 04, 2010 (132)
21 1000GENOMES ss227190196 Jul 14, 2010 (132)
22 1000GENOMES ss236987716 Jul 15, 2010 (132)
23 1000GENOMES ss243335535 Jul 15, 2010 (132)
24 BL ss255583293 May 09, 2011 (134)
25 GMI ss282475355 May 04, 2012 (137)
26 PJP ss291936022 May 09, 2011 (134)
27 ILLUMINA ss481429781 Sep 08, 2015 (146)
28 ILLUMINA ss483302821 May 04, 2012 (137)
29 ILLUMINA ss483491828 May 04, 2012 (137)
30 ILLUMINA ss535518319 Sep 08, 2015 (146)
31 TISHKOFF ss564840276 Apr 25, 2013 (138)
32 SSMP ss660591826 Apr 25, 2013 (138)
33 ILLUMINA ss780226566 Sep 08, 2015 (146)
34 ILLUMINA ss782094496 Sep 08, 2015 (146)
35 ILLUMINA ss835711724 Sep 08, 2015 (146)
36 EVA-GONL ss992381074 Aug 21, 2014 (142)
37 JMKIDD_LAB ss1080554137 Aug 21, 2014 (142)
38 1000GENOMES ss1355772955 Aug 21, 2014 (142)
39 DDI ss1427807830 Apr 01, 2015 (144)
40 EVA_GENOME_DK ss1577875237 Apr 01, 2015 (144)
41 EVA_DECODE ss1696415449 Apr 01, 2015 (144)
42 EVA_SVP ss1713532491 Apr 01, 2015 (144)
43 HAMMER_LAB ss1808465522 Sep 08, 2015 (146)
44 WEILL_CORNELL_DGM ss1935804199 Feb 12, 2016 (147)
45 GENOMED ss1968240800 Jul 19, 2016 (147)
46 JJLAB ss2028689123 Sep 14, 2016 (149)
47 USC_VALOUEV ss2157100224 Dec 20, 2016 (150)
48 HUMAN_LONGEVITY ss2211341108 Dec 20, 2016 (150)
49 TOPMED ss2376090065 Dec 20, 2016 (150)
50 SYSTEMSBIOZJU ss2628837669 Nov 08, 2017 (151)
51 ILLUMINA ss2633305799 Nov 08, 2017 (151)
52 GRF ss2701605783 Nov 08, 2017 (151)
53 GNOMAD ss2941492607 Nov 08, 2017 (151)
54 SWEGEN ss3014243857 Nov 08, 2017 (151)
55 BIOINF_KMB_FNS_UNIBA ss3028167955 Nov 08, 2017 (151)
56 TOPMED ss3242784590 Nov 08, 2017 (151)
57 CSHL ss3351384598 Nov 08, 2017 (151)
58 ILLUMINA ss3627499279 Oct 12, 2018 (152)
59 ILLUMINA ss3631293021 Oct 12, 2018 (152)
60 ILLUMINA ss3636327354 Oct 12, 2018 (152)
61 ILLUMINA ss3641949540 Oct 12, 2018 (152)
62 URBANLAB ss3650487007 Oct 12, 2018 (152)
63 EGCUT_WGS ss3681331035 Jul 13, 2019 (153)
64 EVA_DECODE ss3699031781 Jul 13, 2019 (153)
65 ACPOP ss3741421100 Jul 13, 2019 (153)
66 EVA ss3753802272 Jul 13, 2019 (153)
67 KHV_HUMAN_GENOMES ss3819096732 Jul 13, 2019 (153)
68 1000Genomes NC_000016.9 - 23401076 Oct 12, 2018 (152)
69 Genetic variation in the Estonian population NC_000016.9 - 23401076 Oct 12, 2018 (152)
70 gnomAD - Genomes NC_000016.9 - 23401076 Jul 13, 2019 (153)
71 Northern Sweden NC_000016.9 - 23401076 Jul 13, 2019 (153)
72 A Vietnamese Genetic Variation Database NC_000016.9 - 23401076 Jul 13, 2019 (153)
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)
rs440886 Oct 05, 2000 (86)
rs477443 Oct 05, 2000 (86)
rs52834237 Sep 21, 2007 (128)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss90348376, ss118220584, ss168020587, ss201553332, ss255583293, ss282475355, ss291936022, ss483491828, ss1696415449, ss1713532491 NC_000016.8:23308576:C:T NC_000016.10:23389754:C:T (self)
68920703, 27069283, 188058771, 14705965, 8497445, ss227190196, ss236987716, ss243335535, ss481429781, ss483302821, ss535518319, ss564840276, ss660591826, ss780226566, ss782094496, ss835711724, ss992381074, ss1080554137, ss1355772955, ss1427807830, ss1577875237, ss1808465522, ss1935804199, ss1968240800, ss2028689123, ss2157100224, ss2376090065, ss2628837669, ss2633305799, ss2701605783, ss2941492607, ss3014243857, ss3351384598, ss3627499279, ss3631293021, ss3636327354, ss3641949540, ss3681331035, ss3741421100, ss3753802272 NC_000016.9:23401075:C:T NC_000016.10:23389754:C:T (self)
ss2211341108, ss3028167955, ss3242784590, ss3650487007, ss3699031781, ss3819096732 NC_000016.10:23389754:C:T NC_000016.10:23389754:C:T (self)
ss324670, ss588264, ss646924, ss891023, ss3721900, ss23964723, ss69341600, ss74826547, ss76536853, ss96674760, ss103286492, ss104812637, ss136633509, ss142853613, ss157197686, ss160553877 NT_010393.16:23341075:C:T NC_000016.10:23389754:C:T (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 rs250585

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.post288+114f6e8