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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.

rs114459058

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:232040853 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.002456 (650/264690, TOPMED)
T=0.002288 (321/140278, GnomAD)
T=0.00136 (20/14720, ALFA) (+ 4 more)
T=0.0027 (17/6404, 1000G_30x)
T=0.0028 (14/5008, 1000G)
C=0.5 (1/2, SGDP_PRJ)
T=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TSNAX-DISC1 : Non Coding Transcript Variant
DISC1 : 3 Prime UTR Variant
LOC105373172 : 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 14720 C=0.99864 T=0.00136
European Sub 9824 C=1.0000 T=0.0000
African Sub 2970 C=0.9936 T=0.0064
African Others Sub 114 C=0.982 T=0.018
African American Sub 2856 C=0.9940 T=0.0060
Asian Sub 116 C=1.000 T=0.000
East Asian Sub 88 C=1.00 T=0.00
Other Asian Sub 28 C=1.00 T=0.00
Latin American 1 Sub 154 C=1.000 T=0.000
Latin American 2 Sub 616 C=0.998 T=0.002
South Asian Sub 98 C=1.00 T=0.00
Other Sub 942 C=1.000 T=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 C=0.997544 T=0.002456
gnomAD - Genomes Global Study-wide 140278 C=0.997712 T=0.002288
gnomAD - Genomes European Sub 75960 C=0.99993 T=0.00007
gnomAD - Genomes African Sub 42046 C=0.99325 T=0.00675
gnomAD - Genomes American Sub 13664 C=0.99810 T=0.00190
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2150 C=0.9972 T=0.0028
Allele Frequency Aggregator Total Global 14720 C=0.99864 T=0.00136
Allele Frequency Aggregator European Sub 9824 C=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 2970 C=0.9936 T=0.0064
Allele Frequency Aggregator Other Sub 942 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 2 Sub 616 C=0.998 T=0.002
Allele Frequency Aggregator Latin American 1 Sub 154 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 116 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
1000Genomes_30x Global Study-wide 6404 C=0.9973 T=0.0027
1000Genomes_30x African Sub 1786 C=0.9910 T=0.0090
1000Genomes_30x Europe Sub 1266 C=1.0000 T=0.0000
1000Genomes_30x South Asian Sub 1202 C=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 C=1.0000 T=0.0000
1000Genomes_30x American Sub 980 C=0.999 T=0.001
1000Genomes Global Study-wide 5008 C=0.9972 T=0.0028
1000Genomes African Sub 1322 C=0.9902 T=0.0098
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=1.0000 T=0.0000
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=0.999 T=0.001
SGDP_PRJ Global Study-wide 2 C=0.5 T=0.5
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 1 NC_000001.11:g.232040853C>T
GRCh37.p13 chr 1 NC_000001.10:g.232176599C>T
DISC1 RefSeqGene NG_011681.2:g.419039C>T
Gene: DISC1, DISC1 scaffold protein (plus strand)
Molecule type Change Amino acid[Codon] SO Term
DISC1 transcript variant d NM_001164540.2:c.*4022= N/A 3 Prime UTR Variant
DISC1 transcript variant L NM_018662.3:c.*4022= N/A 3 Prime UTR Variant
DISC1 transcript variant a NM_001164537.2:c.*4022= N/A 3 Prime UTR Variant
DISC1 transcript variant Lv NM_001012957.2:c.*4022= N/A 3 Prime UTR Variant
DISC1 transcript variant Es NM_001012958.2:c. N/A Genic Downstream Transcript Variant
DISC1 transcript variant S NM_001012959.2:c. N/A Genic Downstream Transcript Variant
DISC1 transcript variant b NM_001164538.2:c. N/A Genic Downstream Transcript Variant
DISC1 transcript variant c NM_001164539.2:c. N/A Genic Downstream Transcript Variant
DISC1 transcript variant e NM_001164541.2:c. N/A Genic Downstream Transcript Variant
DISC1 transcript variant f NM_001164542.2:c. N/A Genic Downstream Transcript Variant
DISC1 transcript variant g NM_001164544.2:c. N/A Genic Downstream Transcript Variant
DISC1 transcript variant h NM_001164545.2:c. N/A Genic Downstream Transcript Variant
DISC1 transcript variant i NM_001164546.2:c. N/A Genic Downstream Transcript Variant
DISC1 transcript variant j NM_001164547.2:c. N/A Genic Downstream Transcript Variant
DISC1 transcript variant k NM_001164548.2:c. N/A Genic Downstream Transcript Variant
DISC1 transcript variant l NM_001164549.2:c. N/A Genic Downstream Transcript Variant
DISC1 transcript variant m NM_001164550.2:c. N/A Genic Downstream Transcript Variant
DISC1 transcript variant n NM_001164551.2:c. N/A Genic Downstream Transcript Variant
DISC1 transcript variant o NM_001164552.2:c. N/A Genic Downstream Transcript Variant
DISC1 transcript variant p NM_001164553.2:c. N/A Genic Downstream Transcript Variant
DISC1 transcript variant q NM_001164554.2:c. N/A Genic Downstream Transcript Variant
DISC1 transcript variant r NM_001164555.2:c. N/A Genic Downstream Transcript Variant
DISC1 transcript variant t NM_001164556.2:c. N/A Genic Downstream Transcript Variant
Gene: TSNAX-DISC1, TSNAX-DISC1 readthrough (NMD candidate) (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TSNAX-DISC1 transcript variant 1 NR_028393.1:n.7253C>T N/A Non Coding Transcript Variant
TSNAX-DISC1 transcript variant 2 NR_028394.1:n. N/A Genic Downstream Transcript Variant
TSNAX-DISC1 transcript variant 3 NR_028395.1:n. N/A Genic Downstream Transcript Variant
TSNAX-DISC1 transcript variant 4 NR_028396.1:n. N/A Genic Downstream Transcript Variant
TSNAX-DISC1 transcript variant 5 NR_028397.1:n. N/A Genic Downstream Transcript Variant
TSNAX-DISC1 transcript variant 6 NR_028398.1:n. N/A Genic Downstream Transcript Variant
TSNAX-DISC1 transcript variant 7 NR_028399.1:n. N/A Genic Downstream Transcript Variant
TSNAX-DISC1 transcript variant 8 NR_028400.1:n. N/A Genic Downstream Transcript Variant
Gene: LOC105373172, uncharacterized LOC105373172 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
LOC105373172 transcript XR_001738523.3:n. 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.

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 C= T
GRCh38.p14 chr 1 NC_000001.11:g.232040853= NC_000001.11:g.232040853C>T
GRCh37.p13 chr 1 NC_000001.10:g.232176599= NC_000001.10:g.232176599C>T
DISC1 RefSeqGene NG_011681.2:g.419039= NG_011681.2:g.419039C>T
DISC1 transcript variant L NM_018662.3:c.*4022= NM_018662.3:c.*4022C>T
DISC1 transcript variant L NM_018662.2:c.*4022= NM_018662.2:c.*4022C>T
DISC1 transcript variant a NM_001164537.2:c.*4022= NM_001164537.2:c.*4022C>T
DISC1 transcript variant a NM_001164537.1:c.*4022= NM_001164537.1:c.*4022C>T
DISC1 transcript variant Lv NM_001012957.2:c.*4022= NM_001012957.2:c.*4022C>T
DISC1 transcript variant Lv NM_001012957.1:c.*4022= NM_001012957.1:c.*4022C>T
DISC1 transcript variant d NM_001164540.2:c.*4022= NM_001164540.2:c.*4022C>T
DISC1 transcript variant d NM_001164540.1:c.*4022= NM_001164540.1:c.*4022C>T
TSNAX-DISC1 transcript variant 1 NR_028393.1:n.7253= NR_028393.1:n.7253C>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#.

16 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss218938948 Jul 14, 2010 (132)
2 ILLUMINA ss533971617 Sep 08, 2015 (146)
3 JMKIDD_LAB ss1068686154 Aug 21, 2014 (142)
4 1000GENOMES ss1295072807 Aug 21, 2014 (142)
5 HUMAN_LONGEVITY ss2170958256 Dec 20, 2016 (150)
6 GNOMAD ss2767415660 Nov 08, 2017 (151)
7 ILLUMINA ss3626333188 Oct 11, 2018 (152)
8 SGDP_PRJ ss3851117980 Apr 25, 2020 (154)
9 TOPMED ss4487280514 Apr 25, 2021 (155)
10 1000G_HIGH_COVERAGE ss5246164817 Oct 12, 2022 (156)
11 EVA ss5325465076 Oct 12, 2022 (156)
12 HUGCELL_USP ss5446564108 Oct 12, 2022 (156)
13 1000G_HIGH_COVERAGE ss5520447436 Oct 12, 2022 (156)
14 SANFORD_IMAGENETICS ss5627656383 Oct 12, 2022 (156)
15 EVA ss5912399251 Oct 12, 2022 (156)
16 EVA ss5939504857 Oct 12, 2022 (156)
17 1000Genomes NC_000001.10 - 232176599 Oct 11, 2018 (152)
18 1000Genomes_30x NC_000001.11 - 232040853 Oct 12, 2022 (156)
19 gnomAD - Genomes NC_000001.11 - 232040853 Apr 25, 2021 (155)
20 SGDP_PRJ NC_000001.10 - 232176599 Apr 25, 2020 (154)
21 TopMed NC_000001.11 - 232040853 Apr 25, 2021 (155)
22 ALFA NC_000001.11 - 232040853 Apr 25, 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
5942684, 3134960, ss218938948, ss533971617, ss1068686154, ss1295072807, ss2767415660, ss3626333188, ss3851117980, ss5325465076, ss5627656383, ss5939504857 NC_000001.10:232176598:C:T NC_000001.11:232040852:C:T (self)
7973371, 42626936, 50886849, 2577154232, ss2170958256, ss4487280514, ss5246164817, ss5446564108, ss5520447436, ss5912399251 NC_000001.11:232040852:C:T NC_000001.11:232040852: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 rs114459058

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