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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs4684792

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr3:11652993 (GRCh38.p7) 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
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.24916 (31287/125568, TOPMED)
T=0.2516 (7785/30938, GnomAD)
T=0.285 (1426/5008, 1000G) (+ 2 more)
T=0.263 (1014/3854, ALSPAC)
T=0.255 (944/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
VGLL4 : 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.p7 chr 3 NC_000003.12:g.11652993T>A
GRCh38.p7 chr 3 NC_000003.12:g.11652993T>C
GRCh37.p13 chr 3 NC_000003.11:g.11694467T>A
GRCh37.p13 chr 3 NC_000003.11:g.11694467T>C
Gene: VGLL4, vestigial like family member 4 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
VGLL4 transcript variant 5 NM_001284390.1:c. N/A Intron Variant
VGLL4 transcript variant 2 NM_014667.3:c. N/A Intron Variant
VGLL4 transcript variant 1 NM_001128219.2:c. N/A Genic Upstream Transcript Variant
VGLL4 transcript variant 3 NM_001128220.2:c. N/A Genic Upstream Transcript Variant
VGLL4 transcript variant 4 NM_001128221.2:c. N/A Genic Upstream Transcript Variant
VGLL4 transcript variant 6 NM_001284391.1:c. N/A Genic Upstream Transcript Variant
VGLL4 transcript variant X2 XM_011534267.2:c. N/A Intron Variant
VGLL4 transcript variant X1 XM_017007541.1:c. N/A Intron Variant
VGLL4 transcript variant X6 XM_017007542.1:c. N/A Intron Variant
VGLL4 transcript variant X3 XM_011534268.1:c. N/A Genic Upstream Transcript Variant
VGLL4 transcript variant X5 XM_011534269.1:c. N/A Genic 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.

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").

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Study Population Group Sample Size Ref Allele Alt Allele
Trans-Omics for Precision Medicine Global Study-wide 125568 T=0.24916 C=0.75084
The Genome Aggregation Database Global Study-wide 30938 T=0.2516 C=0.7484
The Genome Aggregation Database European Sub 18484 T=0.2653 C=0.7347
The Genome Aggregation Database African Sub 8716 T=0.200 C=0.800
The Genome Aggregation Database East Asian Sub 1616 T=0.361 C=0.639
The Genome Aggregation Database Other Sub 982 T=0.27 C=0.73
The Genome Aggregation Database American Sub 838 T=0.25 C=0.75
The Genome Aggregation Database Ashkenazi Jewish Sub 302 T=0.28 C=0.72
1000Genomes Global Study-wide 5008 T=0.285 C=0.715
1000Genomes African Sub 1322 T=0.208 C=0.792
1000Genomes East Asian Sub 1008 T=0.382 C=0.618
1000Genomes Europe Sub 1006 T=0.249 C=0.751
1000Genomes South Asian Sub 978 T=0.38 C=0.62
1000Genomes American Sub 694 T=0.20 C=0.80
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.263 C=0.737
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.255 C=0.745
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 C Note
GRCh38.p7 chr 3 NC_000003.12:g.11...

NC_000003.12:g.11652993T=

NC_000003.12:g.11...

NC_000003.12:g.11652993T>A

NC_000003.12:g.11...

NC_000003.12:g.11652993T>C

GRCh37.p13 chr 3 NC_000003.11:g.11...

NC_000003.11:g.11694467T=

NC_000003.11:g.11...

NC_000003.11:g.11694467T>A

NC_000003.11:g.11...

NC_000003.11:g.11694467T>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#.

95 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss6451804 Feb 20, 2003 (111)
2 BCM_SSAHASNP ss10011581 Jul 11, 2003 (116)
3 WI_SSAHASNP ss11529155 Jul 11, 2003 (116)
4 CSHL-HAPMAP ss16972694 Feb 27, 2004 (120)
5 SSAHASNP ss21920294 Apr 05, 2004 (121)
6 PERLEGEN ss23892286 Sep 20, 2004 (123)
7 ABI ss44389108 Mar 14, 2006 (126)
8 ILLUMINA ss67358745 Nov 29, 2006 (127)
9 ILLUMINA ss67746642 Nov 29, 2006 (127)
10 ILLUMINA ss68233321 Dec 12, 2006 (127)
11 PERLEGEN ss68852987 May 16, 2007 (127)
12 ILLUMINA ss70815940 May 26, 2008 (130)
13 ILLUMINA ss71396831 May 16, 2007 (127)
14 ILLUMINA ss75468702 Dec 07, 2007 (129)
15 AFFY ss76582880 Dec 07, 2007 (129)
16 HGSV ss78481627 Dec 07, 2007 (129)
17 KRIBB_YJKIM ss84316415 Dec 16, 2007 (130)
18 BCMHGSC_JDW ss91998947 Mar 24, 2008 (129)
19 HUMANGENOME_JCVI ss99075810 Feb 06, 2009 (130)
20 BGI ss106241900 Feb 06, 2009 (130)
21 1000GENOMES ss111260596 Jan 25, 2009 (130)
22 1000GENOMES ss112085317 Jan 25, 2009 (130)
23 ILLUMINA-UK ss116976285 Feb 14, 2009 (130)
24 ENSEMBL ss135542034 Dec 01, 2009 (131)
25 ENSEMBL ss138724420 Dec 01, 2009 (131)
26 ILLUMINA ss154307554 Dec 01, 2009 (131)
27 GMI ss155109246 Dec 01, 2009 (131)
28 ILLUMINA ss159484339 Dec 01, 2009 (131)
29 ILLUMINA ss160698211 Dec 01, 2009 (131)
30 COMPLETE_GENOMICS ss161922532 Jul 04, 2010 (132)
31 COMPLETE_GENOMICS ss163112808 Jul 04, 2010 (132)
32 COMPLETE_GENOMICS ss166166754 Jul 04, 2010 (132)
33 ILLUMINA ss173779078 Jul 04, 2010 (132)
34 BUSHMAN ss202139611 Jul 04, 2010 (132)
35 1000GENOMES ss219982009 Jul 14, 2010 (132)
36 1000GENOMES ss231709030 Jul 14, 2010 (132)
37 1000GENOMES ss239142908 Jul 15, 2010 (132)
38 BL ss252934351 May 09, 2011 (134)
39 GMI ss277014849 May 04, 2012 (137)
40 GMI ss284595807 Apr 25, 2013 (138)
41 PJP ss292932922 May 09, 2011 (134)
42 ILLUMINA ss481003582 May 04, 2012 (137)
43 ILLUMINA ss481024348 May 04, 2012 (137)
44 ILLUMINA ss482007129 Sep 08, 2015 (146)
45 ILLUMINA ss485296740 May 04, 2012 (137)
46 ILLUMINA ss537258305 Sep 08, 2015 (146)
47 TISHKOFF ss556427572 Apr 25, 2013 (138)
48 SSMP ss650093836 Apr 25, 2013 (138)
49 ILLUMINA ss778542382 Sep 08, 2015 (146)
50 ILLUMINA ss783094238 Sep 08, 2015 (146)
51 ILLUMINA ss784051590 Sep 08, 2015 (146)
52 ILLUMINA ss832352746 Sep 08, 2015 (146)
53 ILLUMINA ss833999023 Sep 08, 2015 (146)
54 EVA-GONL ss978274607 Aug 21, 2014 (142)
55 JMKIDD_LAB ss1070177201 Aug 21, 2014 (142)
56 1000GENOMES ss1302813608 Aug 21, 2014 (142)
57 HAMMER_LAB ss1397329737 Sep 08, 2015 (146)
58 DDI ss1429331437 Apr 01, 2015 (144)
59 EVA_GENOME_DK ss1579846264 Apr 01, 2015 (144)
60 EVA_DECODE ss1587736022 Apr 01, 2015 (144)
61 EVA_UK10K_ALSPAC ss1606419934 Apr 01, 2015 (144)
62 EVA_UK10K_TWINSUK ss1649413967 Apr 01, 2015 (144)
63 EVA_SVP ss1712554059 Apr 01, 2015 (144)
64 ILLUMINA ss1752433775 Sep 08, 2015 (146)
65 HAMMER_LAB ss1798861713 Sep 08, 2015 (146)
66 WEILL_CORNELL_DGM ss1921527101 Feb 12, 2016 (147)
67 GENOMED ss1969324035 Jul 19, 2016 (147)
68 JJLAB ss2021316612 Sep 14, 2016 (149)
69 USC_VALOUEV ss2149384232 Dec 20, 2016 (150)
70 HUMAN_LONGEVITY ss2249098185 Dec 20, 2016 (150)
71 TOPMED ss2416139429 Dec 20, 2016 (150)
72 SYSTEMSBIOZJU ss2625158288 Nov 08, 2017 (151)
73 ILLUMINA ss2633911903 Nov 08, 2017 (151)
74 GRF ss2704744502 Nov 08, 2017 (151)
75 ILLUMINA ss2710965259 Nov 08, 2017 (151)
76 GNOMAD ss2789561106 Nov 08, 2017 (151)
77 SWEGEN ss2991833732 Nov 08, 2017 (151)
78 BIOINF_KMB_FNS_UNIBA ss3024421233 Nov 08, 2017 (151)
79 CSHL ss3344886422 Nov 08, 2017 (151)
80 TOPMED ss3382735439 Nov 08, 2017 (151)
81 TOPMED ss3382735440 Nov 08, 2017 (151)
82 ILLUMINA ss3628590956 Jul 19, 2018 (151)
83 ILLUMINA ss3631860494 Jul 19, 2018 (151)
84 ILLUMINA ss3633282115 Jul 19, 2018 (151)
85 ILLUMINA ss3633998594 Jul 19, 2018 (151)
86 ILLUMINA ss3634880457 Jul 19, 2018 (151)
87 ILLUMINA ss3635682782 Jul 19, 2018 (151)
88 ILLUMINA ss3636576592 Jul 19, 2018 (151)
89 ILLUMINA ss3637435087 Jul 19, 2018 (151)
90 ILLUMINA ss3638397286 Jul 19, 2018 (151)
91 ILLUMINA ss3639202452 Jul 19, 2018 (151)
92 ILLUMINA ss3639902392 Jul 19, 2018 (151)
93 ILLUMINA ss3640587760 Jul 19, 2018 (151)
94 ILLUMINA ss3643355620 Jul 19, 2018 (151)
95 ILLUMINA ss3643949490 Jul 19, 2018 (151)
96 1000Genomes NC_000003.11 - 11694467 Jul 19, 2018 (151)
97 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 11694467 Jul 19, 2018 (151)
98 The Genome Aggregation Database NC_000003.11 - 11694467 Jul 19, 2018 (151)
99 Trans-Omics for Precision Medicine NC_000003.12 - 11652993 Jul 19, 2018 (151)
100 UK 10K study - Twins NC_000003.11 - 11694467 Jul 19, 2018 (151)
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)
rs61468078 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss78481627, ss3639202452, ss3639902392, ss3643949490 NC_000003.9:11669466:T= NC_000003.12:11652992:T= (self)
ss76582880, ss91998947, ss111260596, ss112085317, ss116976285, ss161922532, ss163112808, ss166166754, ss202139611, ss252934351, ss277014849, ss284595807, ss292932922, ss481003582, ss1397329737, ss1587736022, ss1712554059, ss3643355620 NC_000003.10:11669466:T= NC_000003.12:11652992:T= (self)
13958788, 7737435, 130188860, 7737435, ss219982009, ss231709030, ss239142908, ss481024348, ss482007129, ss485296740, ss537258305, ss556427572, ss650093836, ss778542382, ss783094238, ss784051590, ss832352746, ss833999023, ss978274607, ss1070177201, ss1302813608, ss1429331437, ss1579846264, ss1606419934, ss1649413967, ss1752433775, ss1798861713, ss1921527101, ss1969324035, ss2021316612, ss2149384232, ss2416139429, ss2625158288, ss2633911903, ss2704744502, ss2710965259, ss2789561106, ss2991833732, ss3344886422, ss3628590956, ss3631860494, ss3633282115, ss3633998594, ss3634880457, ss3635682782, ss3636576592, ss3637435087, ss3638397286, ss3640587760 NC_000003.11:11694466:T= NC_000003.12:11652992:T= (self)
244716305, ss2249098185, ss3024421233, ss3382735439, ss3382735440 NC_000003.12:11652992:T= NC_000003.12:11652992:T= (self)
ss10011581, ss11529155 NT_005927.15:11623314:T= NC_000003.12:11652992:T= (self)
ss16972694, ss21920294 NT_022517.16:11634466:T= NC_000003.12:11652992:T= (self)
ss6451804, ss23892286, ss44389108, ss67358745, ss67746642, ss68233321, ss68852987, ss70815940, ss71396831, ss75468702, ss84316415, ss99075810, ss106241900, ss135542034, ss138724420, ss154307554, ss155109246, ss159484339, ss160698211, ss173779078 NT_022517.18:11634466:T= NC_000003.12:11652992:T= (self)
ss3382735439 NC_000003.12:11652992:T>A NC_000003.12:11652992:T>A (self)
ss78481627, ss3639202452, ss3639902392, ss3643949490 NC_000003.9:11669466:T>C NC_000003.12:11652992:T>C (self)
ss76582880, ss91998947, ss111260596, ss112085317, ss116976285, ss161922532, ss163112808, ss166166754, ss202139611, ss252934351, ss277014849, ss284595807, ss292932922, ss481003582, ss1397329737, ss1587736022, ss1712554059, ss3643355620 NC_000003.10:11669466:T>C NC_000003.12:11652992:T>C (self)
13958788, 7737435, 130188860, 7737435, ss219982009, ss231709030, ss239142908, ss481024348, ss482007129, ss485296740, ss537258305, ss556427572, ss650093836, ss778542382, ss783094238, ss784051590, ss832352746, ss833999023, ss978274607, ss1070177201, ss1302813608, ss1429331437, ss1579846264, ss1606419934, ss1649413967, ss1752433775, ss1798861713, ss1921527101, ss1969324035, ss2021316612, ss2149384232, ss2416139429, ss2625158288, ss2633911903, ss2704744502, ss2710965259, ss2789561106, ss2991833732, ss3344886422, ss3628590956, ss3631860494, ss3633282115, ss3633998594, ss3634880457, ss3635682782, ss3636576592, ss3637435087, ss3638397286, ss3640587760 NC_000003.11:11694466:T>C NC_000003.12:11652992:T>C (self)
244716305, ss2249098185, ss3024421233, ss3382735440 NC_000003.12:11652992:T>C NC_000003.12:11652992:T>C (self)
ss10011581, ss11529155 NT_005927.15:11623314:T>C NC_000003.12:11652992:T>C (self)
ss16972694, ss21920294 NT_022517.16:11634466:T>C NC_000003.12:11652992:T>C (self)
ss6451804, ss23892286, ss44389108, ss67358745, ss67746642, ss68233321, ss68852987, ss70815940, ss71396831, ss75468702, ss84316415, ss99075810, ss106241900, ss135542034, ss138724420, ss154307554, ss155109246, ss159484339, ss160698211, ss173779078 NT_022517.18:11634466:T>C NC_000003.12:11652992:T>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 rs4684792

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: 0.1.4.post833+d3ba21e