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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.

rs2104054

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr14:67490010 (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
G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.37936 (47636/125568, TOPMED)
G=0.3837 (11923/31076, GnomAD)
G=0.443 (2219/5008, 1000G) (+ 4 more)
G=0.464 (2071/4464, Estonian)
G=0.390 (1502/3854, ALSPAC)
G=0.393 (1458/3708, TWINSUK)
G=0.40 (242/600, NorthernSweden)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TMEM229B : Intron Variant
GPHN : 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 14 NC_000014.9:g.67490010G>T
GRCh37.p13 chr 14 NC_000014.8:g.67956727G>T
Gene: TMEM229B, transmembrane protein 229B (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TMEM229B transcript variant 5 NM_001348544.2:c. N/A Intron Variant
TMEM229B transcript variant 6 NM_001348546.1:c. N/A Intron Variant
TMEM229B transcript variant 7 NM_001348547.2:c. N/A Intron Variant
TMEM229B transcript variant 8 NM_001348548.2:c. N/A Intron Variant
TMEM229B transcript variant 9 NM_001348549.2:c. N/A Intron Variant
TMEM229B transcript variant 4 NM_182526.2:c. N/A Intron Variant
TMEM229B transcript variant 1 NM_001348541.2:c. N/A Genic Upstream Transcript Variant
TMEM229B transcript variant 2 NM_001348542.2:c. N/A Genic Upstream Transcript Variant
TMEM229B transcript variant 3 NM_001348543.2:c. N/A Genic Upstream Transcript Variant
Gene: GPHN, gephyrin (plus strand)
Molecule type Change Amino acid[Codon] SO Term
GPHN transcript variant 2 NM_001024218.1:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant 1 NM_020806.4:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X21 XM_017020925.2:c. N/A Intron Variant
GPHN transcript variant X14 XM_005267254.4:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X1 XM_011536340.3:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X3 XM_011536342.3:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X5 XM_011536343.3:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X6 XM_011536344.3:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X8 XM_011536345.3:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X9 XM_011536346.3:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X15 XM_011536347.2:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X2 XM_017020913.2:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X4 XM_017020914.2:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X7 XM_017020915.2:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X10 XM_017020916.2:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X11 XM_017020917.2:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X12 XM_017020918.2:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X13 XM_017020919.2:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X16 XM_017020920.2:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X17 XM_017020921.1:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X18 XM_017020922.1:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X19 XM_017020923.1:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X20 XM_017020924.1:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X22 XM_017020926.1:c. N/A Genic Downstream 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.

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
TopMed Global Study-wide 125568 G=0.37936 T=0.62064
gnomAD - Genomes Global Study-wide 31076 G=0.3837 T=0.6163
gnomAD - Genomes European Sub 18690 G=0.4114 T=0.5886
gnomAD - Genomes African Sub 8644 G=0.265 T=0.735
gnomAD - Genomes East Asian Sub 1544 G=0.609 T=0.391
gnomAD - Genomes Other Sub 1068 G=0.416 T=0.584
gnomAD - Genomes American Sub 840 G=0.52 T=0.48
gnomAD - Genomes Ashkenazi Jewish Sub 290 G=0.43 T=0.57
1000Genomes Global Study-wide 5008 G=0.443 T=0.557
1000Genomes African Sub 1322 G=0.279 T=0.721
1000Genomes East Asian Sub 1008 G=0.644 T=0.356
1000Genomes Europe Sub 1006 G=0.365 T=0.635
1000Genomes South Asian Sub 978 G=0.52 T=0.48
1000Genomes American Sub 694 G=0.46 T=0.54
Genetic variation in the Estonian population Estonian Study-wide 4464 G=0.464 T=0.536
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.390 T=0.610
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.393 T=0.607
Northern Sweden ACPOP Study-wide 600 G=0.40 T=0.60
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= T Note
GRCh38.p12 chr 14 NC_000014.9:g.67490010= NC_000014.9:g.67490010G>T
GRCh37.p13 chr 14 NC_000014.8:g.67956727= NC_000014.8:g.67956727G>T
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#.

56 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss3022594 Jun 15, 2001 (96)
2 SC_JCM ss6217167 Feb 20, 2003 (111)
3 BCM_SSAHASNP ss10730979 Jul 11, 2003 (116)
4 HGSV ss77452034 Dec 07, 2007 (129)
5 HGSV ss79793544 Dec 15, 2007 (130)
6 HGSV ss82795088 Dec 15, 2007 (130)
7 HGSV ss83465786 Dec 15, 2007 (130)
8 BCMHGSC_JDW ss89980183 Mar 24, 2008 (129)
9 BGI ss103195025 Dec 01, 2009 (131)
10 1000GENOMES ss108419048 Jan 23, 2009 (130)
11 1000GENOMES ss113470272 Jan 25, 2009 (130)
12 ILLUMINA-UK ss118549476 Dec 01, 2009 (131)
13 ENSEMBL ss134026238 Dec 01, 2009 (131)
14 COMPLETE_GENOMICS ss168224093 Jul 04, 2010 (132)
15 COMPLETE_GENOMICS ss169819659 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss171263310 Jul 04, 2010 (132)
17 BUSHMAN ss200208752 Jul 04, 2010 (132)
18 BCM-HGSC-SUB ss207065245 Jul 04, 2010 (132)
19 1000GENOMES ss226625229 Jul 14, 2010 (132)
20 1000GENOMES ss236584061 Jul 15, 2010 (132)
21 1000GENOMES ss243009750 Jul 15, 2010 (132)
22 BL ss255066795 May 09, 2011 (134)
23 GMI ss282045704 May 04, 2012 (137)
24 GMI ss286860872 Apr 25, 2013 (138)
25 PJP ss291620824 May 09, 2011 (134)
26 TISHKOFF ss564158128 Apr 25, 2013 (138)
27 SSMP ss659846612 Apr 25, 2013 (138)
28 EVA-GONL ss991261716 Aug 21, 2014 (142)
29 JMKIDD_LAB ss1079742512 Aug 21, 2014 (142)
30 1000GENOMES ss1351443415 Aug 21, 2014 (142)
31 DDI ss1427456707 Apr 01, 2015 (144)
32 EVA_GENOME_DK ss1577320996 Apr 01, 2015 (144)
33 EVA_UK10K_ALSPAC ss1631971136 Apr 01, 2015 (144)
34 EVA_UK10K_TWINSUK ss1674965169 Apr 01, 2015 (144)
35 HAMMER_LAB ss1807968983 Sep 08, 2015 (146)
36 WEILL_CORNELL_DGM ss1934634980 Feb 12, 2016 (147)
37 GENOMED ss1967987512 Jul 19, 2016 (147)
38 JJLAB ss2028097696 Sep 14, 2016 (149)
39 USC_VALOUEV ss2156473228 Dec 20, 2016 (150)
40 HUMAN_LONGEVITY ss2202895774 Dec 20, 2016 (150)
41 TOPMED ss2367269627 Dec 20, 2016 (150)
42 SYSTEMSBIOZJU ss2628538375 Nov 08, 2017 (151)
43 GRF ss2700903377 Nov 08, 2017 (151)
44 ILLUMINA ss2710802922 Nov 08, 2017 (151)
45 GNOMAD ss2928951650 Nov 08, 2017 (151)
46 BIOINF_KMB_FNS_UNIBA ss3027873414 Nov 08, 2017 (151)
47 TOPMED ss3214074977 Nov 08, 2017 (151)
48 CSHL ss3350858132 Nov 08, 2017 (151)
49 EGCUT_WGS ss3679635935 Jul 13, 2019 (153)
50 EVA_DECODE ss3696896311 Jul 13, 2019 (153)
51 ACPOP ss3740479113 Jul 13, 2019 (153)
52 EVA ss3752456217 Jul 13, 2019 (153)
53 PACBIO ss3787696188 Jul 13, 2019 (153)
54 PACBIO ss3792729768 Jul 13, 2019 (153)
55 PACBIO ss3797614058 Jul 13, 2019 (153)
56 KHV_HUMAN_GENOMES ss3817786749 Jul 13, 2019 (153)
57 1000Genomes NC_000014.8 - 67956727 Oct 12, 2018 (152)
58 The Avon Longitudinal Study of Parents and Children NC_000014.8 - 67956727 Oct 12, 2018 (152)
59 Genetic variation in the Estonian population NC_000014.8 - 67956727 Oct 12, 2018 (152)
60 gnomAD - Genomes NC_000014.8 - 67956727 Jul 13, 2019 (153)
61 Northern Sweden NC_000014.8 - 67956727 Jul 13, 2019 (153)
62 TopMed NC_000014.9 - 67490010 Oct 12, 2018 (152)
63 UK 10K study - Twins NC_000014.8 - 67956727 Oct 12, 2018 (152)
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)
rs60989847 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77452034, ss79793544, ss82795088, ss83465786, ss89980183, ss108419048, ss113470272, ss118549476, ss168224093, ss169819659, ss171263310, ss200208752, ss207065245, ss255066795, ss282045704, ss286860872, ss291620824 NC_000014.7:67026479:G:T NC_000014.9:67490009:G:T (self)
64440932, 35803465, 25374183, 175904659, 13763978, 35803465, ss226625229, ss236584061, ss243009750, ss564158128, ss659846612, ss991261716, ss1079742512, ss1351443415, ss1427456707, ss1577320996, ss1631971136, ss1674965169, ss1807968983, ss1934634980, ss1967987512, ss2028097696, ss2156473228, ss2367269627, ss2628538375, ss2700903377, ss2710802922, ss2928951650, ss3350858132, ss3679635935, ss3740479113, ss3752456217, ss3787696188, ss3792729768, ss3797614058 NC_000014.8:67956726:G:T NC_000014.9:67490009:G:T (self)
118910005, ss2202895774, ss3027873414, ss3214074977, ss3696896311, ss3817786749 NC_000014.9:67490009:G:T NC_000014.9:67490009:G:T (self)
ss10730979 NT_026437.10:47876767:G:T NC_000014.9:67490009:G:T (self)
ss3022594, ss6217167, ss103195025, ss134026238 NT_026437.12:48956726:G:T NC_000014.9:67490009:G: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 rs2104054

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.post308+0fe9b3b