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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.

rs114623325

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:4047106 (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>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.069859 (18491/264690, TOPMED)
A=0.066515 (9189/138150, GnomAD)
A=0.03416 (707/20694, ALFA) (+ 4 more)
A=0.0742 (475/6404, 1000G_30x)
A=0.0691 (346/5008, 1000G)
A=0.046 (10/216, Qatari)
C=0.39 (11/28, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ZBTB7A : 3 Prime UTR 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 20694 C=0.96584 A=0.03416, T=0.00000
European Sub 14308 C=0.99951 A=0.00049, T=0.00000
African Sub 4742 C=0.8568 A=0.1432, T=0.0000
African Others Sub 166 C=0.819 A=0.181, T=0.000
African American Sub 4576 C=0.8582 A=0.1418, T=0.0000
Asian Sub 112 C=1.000 A=0.000, T=0.000
East Asian Sub 86 C=1.00 A=0.00, T=0.00
Other Asian Sub 26 C=1.00 A=0.00, T=0.00
Latin American 1 Sub 134 C=1.000 A=0.000, T=0.000
Latin American 2 Sub 592 C=1.000 A=0.000, T=0.000
South Asian Sub 98 C=1.00 A=0.00, T=0.00
Other Sub 708 C=0.970 A=0.030, 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=0.930141 A=0.069859
gnomAD - Genomes Global Study-wide 138150 C=0.933485 A=0.066515
gnomAD - Genomes European Sub 74984 C=0.99948 A=0.00052
gnomAD - Genomes African Sub 41136 C=0.78809 A=0.21191
gnomAD - Genomes American Sub 13486 C=0.97605 A=0.02395
gnomAD - Genomes Ashkenazi Jewish Sub 3308 C=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3114 C=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2122 C=0.9482 A=0.0518
Allele Frequency Aggregator Total Global 20694 C=0.96584 A=0.03416, T=0.00000
Allele Frequency Aggregator European Sub 14308 C=0.99951 A=0.00049, T=0.00000
Allele Frequency Aggregator African Sub 4742 C=0.8568 A=0.1432, T=0.0000
Allele Frequency Aggregator Other Sub 708 C=0.970 A=0.030, T=0.000
Allele Frequency Aggregator Latin American 2 Sub 592 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 134 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 A=0.00, T=0.00
1000Genomes_30x Global Study-wide 6404 C=0.9258 A=0.0742
1000Genomes_30x African Sub 1786 C=0.7441 A=0.2559
1000Genomes_30x Europe Sub 1266 C=1.0000 A=0.0000
1000Genomes_30x South Asian Sub 1202 C=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 C=1.0000 A=0.0000
1000Genomes_30x American Sub 980 C=0.982 A=0.018
1000Genomes Global Study-wide 5008 C=0.9309 A=0.0691
1000Genomes African Sub 1322 C=0.7481 A=0.2519
1000Genomes East Asian Sub 1008 C=1.0000 A=0.0000
1000Genomes Europe Sub 1006 C=1.0000 A=0.0000
1000Genomes South Asian Sub 978 C=1.000 A=0.000
1000Genomes American Sub 694 C=0.981 A=0.019
Qatari Global Study-wide 216 C=0.954 A=0.046
SGDP_PRJ Global Study-wide 28 C=0.39 A=0.61
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 19 NC_000019.10:g.4047106C>A
GRCh38.p14 chr 19 NC_000019.10:g.4047106C>T
GRCh37.p13 chr 19 NC_000019.9:g.4047104C>A
GRCh37.p13 chr 19 NC_000019.9:g.4047104C>T
Gene: ZBTB7A, zinc finger and BTB domain containing 7A (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ZBTB7A transcript variant 1 NM_015898.4:c.*646= N/A 3 Prime UTR Variant
ZBTB7A transcript variant 2 NM_001317990.2:c.*646= N/A 3 Prime UTR Variant
ZBTB7A transcript variant X1 XM_005259570.6:c.*646= N/A 3 Prime UTR Variant
ZBTB7A transcript variant X2 XM_005259571.5:c.*646= N/A 3 Prime UTR 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= A T
GRCh38.p14 chr 19 NC_000019.10:g.4047106= NC_000019.10:g.4047106C>A NC_000019.10:g.4047106C>T
GRCh37.p13 chr 19 NC_000019.9:g.4047104= NC_000019.9:g.4047104C>A NC_000019.9:g.4047104C>T
ZBTB7A transcript variant X1 XM_005259570.6:c.*646= XM_005259570.6:c.*646G>T XM_005259570.6:c.*646G>A
ZBTB7A transcript variant X1 XM_005259570.5:c.*646= XM_005259570.5:c.*646G>T XM_005259570.5:c.*646G>A
ZBTB7A transcript variant X1 XM_005259570.4:c.*646= XM_005259570.4:c.*646G>T XM_005259570.4:c.*646G>A
ZBTB7A transcript variant X1 XM_005259570.3:c.*646= XM_005259570.3:c.*646G>T XM_005259570.3:c.*646G>A
ZBTB7A transcript variant X1 XM_005259570.2:c.*646= XM_005259570.2:c.*646G>T XM_005259570.2:c.*646G>A
ZBTB7A transcript variant X1 XM_005259570.1:c.*646= XM_005259570.1:c.*646G>T XM_005259570.1:c.*646G>A
ZBTB7A transcript variant X2 XM_005259571.5:c.*646= XM_005259571.5:c.*646G>T XM_005259571.5:c.*646G>A
ZBTB7A transcript variant X2 XM_005259571.4:c.*646= XM_005259571.4:c.*646G>T XM_005259571.4:c.*646G>A
ZBTB7A transcript variant X3 XM_005259571.3:c.*646= XM_005259571.3:c.*646G>T XM_005259571.3:c.*646G>A
ZBTB7A transcript variant X2 XM_005259571.2:c.*646= XM_005259571.2:c.*646G>T XM_005259571.2:c.*646G>A
ZBTB7A transcript variant X2 XM_005259571.1:c.*646= XM_005259571.1:c.*646G>T XM_005259571.1:c.*646G>A
ZBTB7A transcript variant 1 NM_015898.4:c.*646= NM_015898.4:c.*646G>T NM_015898.4:c.*646G>A
ZBTB7A transcript variant 1 NM_015898.3:c.*646= NM_015898.3:c.*646G>T NM_015898.3:c.*646G>A
ZBTB7A transcript NM_015898.2:c.*646= NM_015898.2:c.*646G>T NM_015898.2:c.*646G>A
ZBTB7A transcript variant 2 NM_001317990.2:c.*646= NM_001317990.2:c.*646G>T NM_001317990.2:c.*646G>A
ZBTB7A transcript variant 2 NM_001317990.1:c.*646= NM_001317990.1:c.*646G>T NM_001317990.1:c.*646G>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#.

18 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss228017181 Jul 14, 2010 (132)
2 ILLUMINA ss482323711 May 04, 2012 (137)
3 ILLUMINA ss483821228 May 04, 2012 (137)
4 ILLUMINA ss781723746 Sep 08, 2015 (146)
5 1000GENOMES ss1362145475 Aug 21, 2014 (142)
6 WEILL_CORNELL_DGM ss1937511267 Feb 12, 2016 (147)
7 HUMAN_LONGEVITY ss2223873087 Dec 20, 2016 (150)
8 GNOMAD ss2959848937 Nov 08, 2017 (151)
9 KHV_HUMAN_GENOMES ss3821001385 Jul 13, 2019 (153)
10 SGDP_PRJ ss3887642532 Apr 27, 2020 (154)
11 TOPMED ss5066282429 Apr 26, 2021 (155)
12 1000G_HIGH_COVERAGE ss5306293714 Oct 16, 2022 (156)
13 EVA ss5433237028 Oct 16, 2022 (156)
14 HUGCELL_USP ss5498951461 Oct 16, 2022 (156)
15 1000G_HIGH_COVERAGE ss5611617487 Oct 16, 2022 (156)
16 SANFORD_IMAGENETICS ss5661868082 Oct 16, 2022 (156)
17 EVA ss5927091254 Oct 16, 2022 (156)
18 EVA ss5953295928 Oct 16, 2022 (156)
19 1000Genomes NC_000019.9 - 4047104 Oct 12, 2018 (152)
20 1000Genomes_30x NC_000019.10 - 4047106 Oct 16, 2022 (156)
21 gnomAD - Genomes NC_000019.10 - 4047106 Apr 26, 2021 (155)
22 Qatari NC_000019.9 - 4047104 Apr 27, 2020 (154)
23 SGDP_PRJ NC_000019.9 - 4047104 Apr 27, 2020 (154)
24 TopMed NC_000019.10 - 4047106 Apr 26, 2021 (155)
25 ALFA NC_000019.10 - 4047106 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss483821228 NC_000019.8:3998103:C:A NC_000019.10:4047105:C:A (self)
75514653, 19553189, 39659512, ss228017181, ss482323711, ss781723746, ss1362145475, ss1937511267, ss2959848937, ss3887642532, ss5433237028, ss5661868082, ss5953295928 NC_000019.9:4047103:C:A NC_000019.10:4047105:C:A (self)
99143422, 532548284, 281828093, 12333437446, ss2223873087, ss3821001385, ss5066282429, ss5306293714, ss5498951461, ss5611617487, ss5927091254 NC_000019.10:4047105:C:A NC_000019.10:4047105:C:A (self)
12333437446 NC_000019.10:4047105:C:T NC_000019.10:4047105: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 rs114623325

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