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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.

rs114558470

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr8:41648385 (GRCh38.p13) 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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.008844 (2341/264690, TOPMED)
A=0.008166 (1145/140216, GnomAD)
A=0.00319 (82/25702, ALFA) (+ 1 more)
A=0.0054 (27/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NKX6-3 : 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.p13 chr 8 NC_000008.11:g.41648385G>A
GRCh37.p13 chr 8 NC_000008.10:g.41505904G>A
Gene: NKX6-3, NK6 homeobox 3 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
NKX6-3 transcript variant 1 NM_001364841.2:c.383-150C…

NM_001364841.2:c.383-150C>T

N/A Intron Variant
NKX6-3 transcript variant 2 NM_152568.3: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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 25702 G=0.99681 A=0.00319
European Sub 20226 G=0.99995 A=0.00005
African Sub 3168 G=0.9766 A=0.0234
African Others Sub 124 G=1.000 A=0.000
African American Sub 3044 G=0.9757 A=0.0243
Asian Sub 128 G=1.000 A=0.000
East Asian Sub 100 G=1.00 A=0.00
Other Asian Sub 28 G=1.00 A=0.00
Latin American 1 Sub 168 G=1.000 A=0.000
Latin American 2 Sub 700 G=0.999 A=0.001
South Asian Sub 114 G=1.000 A=0.000
Other Sub 1198 G=0.9950 A=0.0050


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=0.991156 A=0.008844
gnomAD - Genomes Global Study-wide 140216 G=0.991834 A=0.008166
gnomAD - Genomes European Sub 75926 G=0.99995 A=0.00005
gnomAD - Genomes African Sub 42032 G=0.97411 A=0.02589
gnomAD - Genomes American Sub 13652 G=0.99802 A=0.00198
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3132 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2150 G=0.9879 A=0.0121
1000Genomes Global Study-wide 5008 G=0.9946 A=0.0054
1000Genomes African Sub 1322 G=0.9796 A=0.0204
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=1.000 A=0.000
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
GRCh38.p13 chr 8 NC_000008.11:g.41648385= NC_000008.11:g.41648385G>A
GRCh37.p13 chr 8 NC_000008.10:g.41505904= NC_000008.10:g.41505904G>A
NKX6-3 transcript variant 1 NM_001364841.2:c.383-150= NM_001364841.2:c.383-150C>T
NKX6-3 transcript variant X1 XM_005273422.1:c.383-150= XM_005273422.1:c.383-150C>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#.

21 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss223671598 Jul 14, 2010 (132)
2 ILLUMINA ss482805905 May 04, 2012 (137)
3 ILLUMINA ss485620380 May 04, 2012 (137)
4 ILLUMINA ss534780610 Sep 08, 2015 (146)
5 TISHKOFF ss560707181 Apr 25, 2013 (138)
6 ILLUMINA ss780075106 Sep 08, 2015 (146)
7 ILLUMINA ss781883727 Sep 08, 2015 (146)
8 ILLUMINA ss835556949 Sep 08, 2015 (146)
9 1000GENOMES ss1329554846 Aug 21, 2014 (142)
10 HUMAN_LONGEVITY ss2302632610 Dec 20, 2016 (150)
11 TOPMED ss2472290868 Dec 20, 2016 (150)
12 ILLUMINA ss2634740574 Nov 08, 2017 (151)
13 GNOMAD ss2865900875 Nov 08, 2017 (151)
14 TOPMED ss3560031121 Nov 08, 2017 (151)
15 ILLUMINA ss3630048121 Oct 12, 2018 (152)
16 ILLUMINA ss3632639983 Oct 12, 2018 (152)
17 ILLUMINA ss3642627873 Oct 12, 2018 (152)
18 EVA_DECODE ss3721876455 Jul 13, 2019 (153)
19 EVA ss3767913642 Jul 13, 2019 (153)
20 KHV_HUMAN_GENOMES ss3811074291 Jul 13, 2019 (153)
21 TOPMED ss4783539467 Apr 26, 2021 (155)
22 1000Genomes NC_000008.10 - 41505904 Oct 12, 2018 (152)
23 gnomAD - Genomes NC_000008.11 - 41648385 Apr 26, 2021 (155)
24 TopMed NC_000008.11 - 41648385 Apr 26, 2021 (155)
25 ALFA NC_000008.11 - 41648385 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
ss485620380 NC_000008.9:41625060:G:A NC_000008.11:41648384:G:A (self)
41670755, ss223671598, ss482805905, ss534780610, ss560707181, ss780075106, ss781883727, ss835556949, ss1329554846, ss2472290868, ss2634740574, ss2865900875, ss3630048121, ss3632639983, ss3642627873, ss3767913642 NC_000008.10:41505903:G:A NC_000008.11:41648384:G:A (self)
293819709, 388036150, 620917027, 8261685348, ss2302632610, ss3560031121, ss3721876455, ss3811074291, ss4783539467 NC_000008.11:41648384:G:A NC_000008.11:41648384:G:A (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 rs114558470

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.post596+ae089ad