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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.

rs12894760

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr14:67662860 (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
A=0.227258 (60153/264690, TOPMED)
A=0.208576 (27749/133040, GnomAD)
G=0.43615 (12323/28254, 14KJPN) (+ 15 more)
A=0.16781 (3094/18438, ALFA)
G=0.44217 (7409/16756, 8.3KJPN)
A=0.3303 (2115/6404, 1000G_30x)
A=0.3349 (1677/5008, 1000G)
A=0.1151 (515/4476, Estonian)
A=0.1549 (597/3854, ALSPAC)
A=0.1505 (558/3708, TWINSUK)
A=0.4713 (1381/2930, KOREAN)
A=0.4760 (872/1832, Korea1K)
A=0.151 (151/998, GoNL)
A=0.152 (91/600, NorthernSweden)
G=0.345 (100/290, SGDP_PRJ)
A=0.245 (53/216, Qatari)
A=0.23 (9/40, GENOME_DK)
G=0.45 (9/20, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GPHN : Intron Variant
VTI1B : 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 18438 G=0.83219 A=0.16781, C=0.00000
European Sub 14070 G=0.85672 A=0.14328, C=0.00000
African Sub 2710 G=0.7871 A=0.2129, C=0.0000
African Others Sub 98 G=0.80 A=0.20, C=0.00
African American Sub 2612 G=0.7868 A=0.2132, C=0.0000
Asian Sub 112 G=0.562 A=0.438, C=0.000
East Asian Sub 86 G=0.53 A=0.47, C=0.00
Other Asian Sub 26 G=0.65 A=0.35, C=0.00
Latin American 1 Sub 146 G=0.733 A=0.267, C=0.000
Latin American 2 Sub 610 G=0.652 A=0.348, C=0.000
South Asian Sub 98 G=0.58 A=0.42, C=0.00
Other Sub 692 G=0.769 A=0.231, 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=0.772742 A=0.227258
gnomAD - Genomes Global Study-wide 133040 G=0.791424 A=0.208576
gnomAD - Genomes European Sub 73248 G=0.83488 A=0.16512
gnomAD - Genomes African Sub 38842 G=0.75959 A=0.24041
gnomAD - Genomes American Sub 12550 G=0.68845 A=0.31155
gnomAD - Genomes Ashkenazi Jewish Sub 3296 G=0.8322 A=0.1678
gnomAD - Genomes East Asian Sub 3074 G=0.5514 A=0.4486
gnomAD - Genomes Other Sub 2030 G=0.7665 A=0.2335
14KJPN JAPANESE Study-wide 28254 G=0.43615 A=0.56385
Allele Frequency Aggregator Total Global 18438 G=0.83219 A=0.16781, C=0.00000
Allele Frequency Aggregator European Sub 14070 G=0.85672 A=0.14328, C=0.00000
Allele Frequency Aggregator African Sub 2710 G=0.7871 A=0.2129, C=0.0000
Allele Frequency Aggregator Other Sub 692 G=0.769 A=0.231, C=0.000
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.652 A=0.348, C=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.733 A=0.267, C=0.000
Allele Frequency Aggregator Asian Sub 112 G=0.562 A=0.438, C=0.000
Allele Frequency Aggregator South Asian Sub 98 G=0.58 A=0.42, C=0.00
8.3KJPN JAPANESE Study-wide 16756 G=0.44217 A=0.55783
1000Genomes_30x Global Study-wide 6404 G=0.6697 A=0.3303
1000Genomes_30x African Sub 1786 G=0.7424 A=0.2576
1000Genomes_30x Europe Sub 1266 G=0.8112 A=0.1888
1000Genomes_30x South Asian Sub 1202 G=0.5208 A=0.4792
1000Genomes_30x East Asian Sub 1170 G=0.5316 A=0.4684
1000Genomes_30x American Sub 980 G=0.702 A=0.298
1000Genomes Global Study-wide 5008 G=0.6651 A=0.3349
1000Genomes African Sub 1322 G=0.7451 A=0.2549
1000Genomes East Asian Sub 1008 G=0.5258 A=0.4742
1000Genomes Europe Sub 1006 G=0.8121 A=0.1879
1000Genomes South Asian Sub 978 G=0.521 A=0.479
1000Genomes American Sub 694 G=0.705 A=0.295
Genetic variation in the Estonian population Estonian Study-wide 4476 G=0.8849 A=0.1151
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.8451 A=0.1549
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.8495 A=0.1505
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.5287 A=0.4713
Korean Genome Project KOREAN Study-wide 1832 G=0.5240 A=0.4760
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.849 A=0.151
Northern Sweden ACPOP Study-wide 600 G=0.848 A=0.152
SGDP_PRJ Global Study-wide 290 G=0.345 A=0.655
Qatari Global Study-wide 216 G=0.755 A=0.245
The Danish reference pan genome Danish Study-wide 40 G=0.78 A=0.23
Siberian Global Study-wide 20 G=0.45 A=0.55
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 14 NC_000014.9:g.67662860G>A
GRCh38.p14 chr 14 NC_000014.9:g.67662860G>C
GRCh37.p13 chr 14 NC_000014.8:g.68129577G>A
GRCh37.p13 chr 14 NC_000014.8:g.68129577G>C
Gene: VTI1B, vesicle transport through interaction with t-SNAREs 1B (minus strand)
Molecule type Change Amino acid[Codon] SO Term
VTI1B transcript NM_006370.3:c.116-325C>T N/A Intron Variant
Gene: GPHN, gephyrin (plus strand)
Molecule type Change Amino acid[Codon] SO Term
GPHN transcript variant 2 NM_001024218.2:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant 3 NM_001377514.1:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant 4 NM_001377515.1:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant 5 NM_001377516.1:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant 6 NM_001377517.1:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant 7 NM_001377518.1:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant 8 NM_001377519.1:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant 1 NM_020806.5:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X14 XM_047430879.1:c.1313-723…

XM_047430879.1:c.1313-72335G>A

 		N/A Intron Variant
GPHN transcript variant X1 XM_011536340.4:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X3 XM_011536342.4:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X5 XM_011536343.4:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X7 XM_011536344.4:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X9 XM_011536345.4:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X2 XM_017020913.3:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X4 XM_017020914.3:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X10 XM_017020917.3:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X11 XM_017020918.3:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X6 XM_047430875.1:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X8 XM_047430876.1:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X12 XM_047430877.1:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X13 XM_047430878.1:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X15 XM_047430880.1: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

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 14 NC_000014.9:g.67662860= NC_000014.9:g.67662860G>A NC_000014.9:g.67662860G>C
GRCh37.p13 chr 14 NC_000014.8:g.68129577= NC_000014.8:g.68129577G>A NC_000014.8:g.68129577G>C
VTI1B transcript NM_006370.2:c.116-325= NM_006370.2:c.116-325C>T NM_006370.2:c.116-325C>G
VTI1B transcript NM_006370.3:c.116-325= NM_006370.3:c.116-325C>T NM_006370.3:c.116-325C>G
VTI1B transcript variant X1 XM_005267264.1:c.116-325= XM_005267264.1:c.116-325C>T XM_005267264.1:c.116-325C>G
VTI1B transcript variant X2 XM_005267265.1:c.52-2938= XM_005267265.1:c.52-2938C>T XM_005267265.1:c.52-2938C>G
VTI1B transcript variant X3 XM_005267266.1:c.-69+169= XM_005267266.1:c.-69+169C>T XM_005267266.1:c.-69+169C>G
GPHN transcript variant X14 XM_047430879.1:c.1313-72335= XM_047430879.1:c.1313-72335G>A XM_047430879.1:c.1313-72335G>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#.

57 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss21215337 Apr 05, 2004 (121)
2 ABI ss40464730 Mar 15, 2006 (126)
3 HGSV ss85990052 Dec 15, 2007 (130)
4 HGSV ss85995002 Dec 15, 2007 (130)
5 HUMANGENOME_JCVI ss96865850 Feb 04, 2009 (130)
6 ENSEMBL ss137011951 Dec 01, 2009 (131)
7 COMPLETE_GENOMICS ss169822200 Jul 04, 2010 (132)
8 BUSHMAN ss200210248 Jul 04, 2010 (132)
9 GMI ss282046326 May 04, 2012 (137)
10 PJP ss291621075 May 09, 2011 (134)
11 1000GENOMES ss338418284 May 09, 2011 (134)
12 TISHKOFF ss564158987 Apr 25, 2013 (138)
13 SSMP ss659847562 Apr 25, 2013 (138)
14 EVA-GONL ss991263126 Aug 21, 2014 (142)
15 JMKIDD_LAB ss1079743590 Aug 21, 2014 (142)
16 1000GENOMES ss1351448250 Aug 21, 2014 (142)
17 DDI ss1427457104 Apr 01, 2015 (144)
18 EVA_GENOME_DK ss1577321750 Apr 01, 2015 (144)
19 EVA_UK10K_ALSPAC ss1631973832 Apr 01, 2015 (144)
20 EVA_UK10K_TWINSUK ss1674967865 Apr 01, 2015 (144)
21 EVA_DECODE ss1695267488 Apr 01, 2015 (144)
22 HAMMER_LAB ss1807969561 Sep 08, 2015 (146)
23 WEILL_CORNELL_DGM ss1934636277 Feb 12, 2016 (147)
24 JJLAB ss2028098421 Sep 14, 2016 (149)
25 USC_VALOUEV ss2156474068 Dec 20, 2016 (150)
26 HUMAN_LONGEVITY ss2202905577 Dec 20, 2016 (150)
27 SYSTEMSBIOZJU ss2628538801 Nov 08, 2017 (151)
28 GRF ss2700904233 Nov 08, 2017 (151)
29 GNOMAD ss2928964570 Nov 08, 2017 (151)
30 SWEGEN ss3012382857 Nov 08, 2017 (151)
31 BIOINF_KMB_FNS_UNIBA ss3027873822 Nov 08, 2017 (151)
32 CSHL ss3350858661 Nov 08, 2017 (151)
33 URBANLAB ss3650229094 Oct 12, 2018 (152)
34 EGCUT_WGS ss3679638064 Jul 13, 2019 (153)
35 EVA_DECODE ss3696898728 Jul 13, 2019 (153)
36 ACPOP ss3740480219 Jul 13, 2019 (153)
37 EVA ss3752457770 Jul 13, 2019 (153)
38 KHV_HUMAN_GENOMES ss3817788348 Jul 13, 2019 (153)
39 EVA ss3833975523 Apr 27, 2020 (154)
40 SGDP_PRJ ss3881740131 Apr 27, 2020 (154)
41 KRGDB ss3930780082 Apr 27, 2020 (154)
42 KOGIC ss3975148166 Apr 27, 2020 (154)
43 TOPMED ss4974518443 Apr 26, 2021 (155)
44 TOMMO_GENOMICS ss5213735699 Apr 26, 2021 (155)
45 1000G_HIGH_COVERAGE ss5296613153 Oct 16, 2022 (156)
46 EVA ss5415970977 Oct 16, 2022 (156)
47 HUGCELL_USP ss5490618026 Oct 16, 2022 (156)
48 EVA ss5511282594 Oct 16, 2022 (156)
49 1000G_HIGH_COVERAGE ss5597091318 Oct 16, 2022 (156)
50 SANFORD_IMAGENETICS ss5656441464 Oct 16, 2022 (156)
51 TOMMO_GENOMICS ss5766683661 Oct 16, 2022 (156)
52 YY_MCH ss5814848184 Oct 16, 2022 (156)
53 EVA ss5841262394 Oct 16, 2022 (156)
54 EVA ss5851081406 Oct 16, 2022 (156)
55 EVA ss5901787526 Oct 16, 2022 (156)
56 EVA ss5947884291 Oct 16, 2022 (156)
57 EVA ss5980833593 Oct 16, 2022 (156)
58 1000Genomes NC_000014.8 - 68129577 Oct 12, 2018 (152)
59 1000Genomes_30x NC_000014.9 - 67662860 Oct 16, 2022 (156)
60 The Avon Longitudinal Study of Parents and Children NC_000014.8 - 68129577 Oct 12, 2018 (152)
61 Genetic variation in the Estonian population NC_000014.8 - 68129577 Oct 12, 2018 (152)
62 The Danish reference pan genome NC_000014.8 - 68129577 Apr 27, 2020 (154)
63 gnomAD - Genomes NC_000014.9 - 67662860 Apr 26, 2021 (155)
64 Genome of the Netherlands Release 5 NC_000014.8 - 68129577 Apr 27, 2020 (154)
65 KOREAN population from KRGDB NC_000014.8 - 68129577 Apr 27, 2020 (154)
66 Korean Genome Project NC_000014.9 - 67662860 Apr 27, 2020 (154)
67 Northern Sweden NC_000014.8 - 68129577 Jul 13, 2019 (153)
68 Qatari NC_000014.8 - 68129577 Apr 27, 2020 (154)
69 SGDP_PRJ NC_000014.8 - 68129577 Apr 27, 2020 (154)
70 Siberian NC_000014.8 - 68129577 Apr 27, 2020 (154)
71 8.3KJPN NC_000014.8 - 68129577 Apr 26, 2021 (155)
72 14KJPN NC_000014.9 - 67662860 Oct 16, 2022 (156)
73 TopMed NC_000014.9 - 67662860 Apr 26, 2021 (155)
74 UK 10K study - Twins NC_000014.8 - 68129577 Oct 12, 2018 (152)
75 ALFA NC_000014.9 - 67662860 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)
rs58232538 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss85990052, ss85995002, ss169822200, ss200210248, ss282046326, ss291621075, ss1695267488 NC_000014.7:67199329:G:A NC_000014.9:67662859:G:A (self)
64445962, 35806441, 25376312, 3649449, 15991070, 37957476, 13765084, 16678207, 33757111, 8990422, 71705006, 35806441, ss338418284, ss564158987, ss659847562, ss991263126, ss1079743590, ss1351448250, ss1427457104, ss1577321750, ss1631973832, ss1674967865, ss1807969561, ss1934636277, ss2028098421, ss2156474068, ss2628538801, ss2700904233, ss2928964570, ss3012382857, ss3350858661, ss3679638064, ss3740480219, ss3752457770, ss3833975523, ss3881740131, ss3930780082, ss5213735699, ss5415970977, ss5511282594, ss5656441464, ss5841262394, ss5947884291, ss5980833593 NC_000014.8:68129576:G:A NC_000014.9:67662859:G:A (self)
84617253, 454408776, 31526167, 100520765, 190064102, 11720566418, ss2202905577, ss3027873822, ss3650229094, ss3696898728, ss3817788348, ss3975148166, ss4974518443, ss5296613153, ss5490618026, ss5597091318, ss5766683661, ss5814848184, ss5851081406, ss5901787526 NC_000014.9:67662859:G:A NC_000014.9:67662859:G:A (self)
ss21215337 NT_026437.10:48049617:G:A NC_000014.9:67662859:G:A (self)
ss40464730, ss96865850, ss137011951 NT_026437.12:49129576:G:A NC_000014.9:67662859:G:A (self)
11720566418 NC_000014.9:67662859:G:C NC_000014.9:67662859: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 rs12894760

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