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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.

rs117192202

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr14:67774536 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.013854 (3667/264690, TOPMED)
A=0.013806 (1933/140010, GnomAD)
A=0.01657 (313/18890, ALFA) (+ 11 more)
A=0.0087 (56/6404, 1000G_30x)
A=0.0086 (43/5008, 1000G)
A=0.0161 (72/4480, Estonian)
A=0.0169 (65/3854, ALSPAC)
A=0.0159 (59/3708, TWINSUK)
A=0.022 (22/998, GoNL)
A=0.010 (6/600, NorthernSweden)
A=0.023 (5/216, Qatari)
G=0.4 (4/10, SGDP_PRJ)
G=0.5 (1/2, Siberian)
A=0.5 (1/2, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ZFYVE26 : 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 18890 G=0.98343 A=0.01657
European Sub 14286 G=0.98061 A=0.01939
African Sub 2946 G=0.9949 A=0.0051
African Others Sub 114 G=1.000 A=0.000
African American Sub 2832 G=0.9947 A=0.0053
Asian Sub 112 G=1.000 A=0.000
East Asian Sub 86 G=1.00 A=0.00
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 146 G=0.986 A=0.014
Latin American 2 Sub 610 G=0.992 A=0.008
South Asian Sub 98 G=0.97 A=0.03
Other Sub 692 G=0.984 A=0.016


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=0.986146 A=0.013854
gnomAD - Genomes Global Study-wide 140010 G=0.986194 A=0.013806
gnomAD - Genomes European Sub 75806 G=0.98119 A=0.01881
gnomAD - Genomes African Sub 41970 G=0.99643 A=0.00357
gnomAD - Genomes American Sub 13638 G=0.98731 A=0.01269
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.9521 A=0.0479
gnomAD - Genomes East Asian Sub 3128 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2146 G=0.9884 A=0.0116
Allele Frequency Aggregator Total Global 18890 G=0.98343 A=0.01657
Allele Frequency Aggregator European Sub 14286 G=0.98061 A=0.01939
Allele Frequency Aggregator African Sub 2946 G=0.9949 A=0.0051
Allele Frequency Aggregator Other Sub 692 G=0.984 A=0.016
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.992 A=0.008
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.986 A=0.014
Allele Frequency Aggregator Asian Sub 112 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=0.97 A=0.03
1000Genomes_30x Global Study-wide 6404 G=0.9913 A=0.0087
1000Genomes_30x African Sub 1786 G=1.0000 A=0.0000
1000Genomes_30x Europe Sub 1266 G=0.9700 A=0.0300
1000Genomes_30x South Asian Sub 1202 G=0.9942 A=0.0058
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000
1000Genomes_30x American Sub 980 G=0.989 A=0.011
1000Genomes Global Study-wide 5008 G=0.9914 A=0.0086
1000Genomes African Sub 1322 G=1.0000 A=0.0000
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=0.9682 A=0.0318
1000Genomes South Asian Sub 978 G=0.996 A=0.004
1000Genomes American Sub 694 G=0.990 A=0.010
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9839 A=0.0161
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9831 A=0.0169
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9841 A=0.0159
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.978 A=0.022
Northern Sweden ACPOP Study-wide 600 G=0.990 A=0.010
Qatari Global Study-wide 216 G=0.977 A=0.023
SGDP_PRJ Global Study-wide 10 G=0.4 A=0.6
Siberian Global Study-wide 2 G=0.5 A=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 14 NC_000014.9:g.67774536G>A
GRCh37.p13 chr 14 NC_000014.8:g.68241253G>A
ZFYVE26 RefSeqGene NG_011836.1:g.47054C>T
Gene: ZFYVE26, zinc finger FYVE-type containing 26 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ZFYVE26 transcript NM_015346.4:c.5320+480C>T N/A Intron Variant
ZFYVE26 transcript variant X1 XM_047431173.1:c.5320+480…

XM_047431173.1:c.5320+480C>T

N/A Intron Variant
ZFYVE26 transcript variant X2 XM_047431174.1:c.2995+480…

XM_047431174.1:c.2995+480C>T

N/A Intron Variant
ZFYVE26 transcript variant X3 XM_047431175.1:c.2902+480…

XM_047431175.1:c.2902+480C>T

N/A Intron Variant
ZFYVE26 transcript variant X4 XM_011536609.3: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
GRCh38.p14 chr 14 NC_000014.9:g.67774536= NC_000014.9:g.67774536G>A
GRCh37.p13 chr 14 NC_000014.8:g.68241253= NC_000014.8:g.68241253G>A
ZFYVE26 RefSeqGene NG_011836.1:g.47054= NG_011836.1:g.47054C>T
ZFYVE26 transcript NM_015346.3:c.5320+480= NM_015346.3:c.5320+480C>T
ZFYVE26 transcript NM_015346.4:c.5320+480= NM_015346.4:c.5320+480C>T
ZFYVE26 transcript variant X1 XM_047431173.1:c.5320+480= XM_047431173.1:c.5320+480C>T
ZFYVE26 transcript variant X2 XM_047431174.1:c.2995+480= XM_047431174.1:c.2995+480C>T
ZFYVE26 transcript variant X3 XM_047431175.1:c.2902+480= XM_047431175.1:c.2902+480C>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#.

28 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss236584845 Jul 15, 2010 (132)
2 SSMP ss659848109 Apr 25, 2013 (138)
3 EVA-GONL ss991263896 Aug 21, 2014 (142)
4 1000GENOMES ss1351451132 Aug 21, 2014 (142)
5 EVA_UK10K_ALSPAC ss1631975510 Apr 01, 2015 (144)
6 EVA_UK10K_TWINSUK ss1674969543 Apr 01, 2015 (144)
7 EVA_DECODE ss1695268313 Apr 01, 2015 (144)
8 WEILL_CORNELL_DGM ss1934636979 Feb 12, 2016 (147)
9 USC_VALOUEV ss2156474529 Dec 20, 2016 (150)
10 HUMAN_LONGEVITY ss2202911720 Dec 20, 2016 (150)
11 GNOMAD ss2928972911 Nov 08, 2017 (151)
12 SWEGEN ss3012384115 Nov 08, 2017 (151)
13 EGCUT_WGS ss3679639314 Jul 13, 2019 (153)
14 EVA_DECODE ss3696900323 Jul 13, 2019 (153)
15 ACPOP ss3740480829 Jul 13, 2019 (153)
16 SGDP_PRJ ss3881741757 Apr 27, 2020 (154)
17 TOPMED ss4974543827 Apr 26, 2021 (155)
18 EVA ss5237541458 Apr 26, 2021 (155)
19 1000G_HIGH_COVERAGE ss5296615745 Oct 16, 2022 (156)
20 EVA ss5415975538 Oct 16, 2022 (156)
21 HUGCELL_USP ss5490620354 Oct 16, 2022 (156)
22 1000G_HIGH_COVERAGE ss5597095007 Oct 16, 2022 (156)
23 SANFORD_IMAGENETICS ss5656442798 Oct 16, 2022 (156)
24 EVA ss5841263562 Oct 16, 2022 (156)
25 EVA ss5847439158 Oct 16, 2022 (156)
26 EVA ss5901790524 Oct 16, 2022 (156)
27 EVA ss5947885796 Oct 16, 2022 (156)
28 EVA ss5979444209 Oct 16, 2022 (156)
29 1000Genomes NC_000014.8 - 68241253 Oct 12, 2018 (152)
30 1000Genomes_30x NC_000014.9 - 67774536 Oct 16, 2022 (156)
31 The Avon Longitudinal Study of Parents and Children NC_000014.8 - 68241253 Oct 12, 2018 (152)
32 Genetic variation in the Estonian population NC_000014.8 - 68241253 Oct 12, 2018 (152)
33 gnomAD - Genomes NC_000014.9 - 67774536 Apr 26, 2021 (155)
34 Genome of the Netherlands Release 5 NC_000014.8 - 68241253 Apr 27, 2020 (154)
35 Northern Sweden NC_000014.8 - 68241253 Jul 13, 2019 (153)
36 Qatari NC_000014.8 - 68241253 Apr 27, 2020 (154)
37 SGDP_PRJ NC_000014.8 - 68241253 Apr 27, 2020 (154)
38 Siberian NC_000014.8 - 68241253 Apr 27, 2020 (154)
39 TopMed NC_000014.9 - 67774536 Apr 26, 2021 (155)
40 UK 10K study - Twins NC_000014.8 - 68241253 Oct 12, 2018 (152)
41 ALFA NC_000014.9 - 67774536 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
ss1695268313 NC_000014.7:67311005:G:A NC_000014.9:67774535:G:A (self)
64448960, 35808309, 25377562, 15991818, 13765694, 16678909, 33758737, 8990883, 35808309, ss236584845, ss659848109, ss991263896, ss1351451132, ss1631975510, ss1674969543, ss1934636979, ss2156474529, ss2928972911, ss3012384115, ss3679639314, ss3740480829, ss3881741757, ss5237541458, ss5415975538, ss5656442798, ss5841263562, ss5847439158, ss5947885796, ss5979444209 NC_000014.8:68241252:G:A NC_000014.9:67774535:G:A (self)
84620942, 454430108, 190089486, 12916130596, ss2202911720, ss3696900323, ss4974543827, ss5296615745, ss5490620354, ss5597095007, ss5901790524 NC_000014.9:67774535:G:A NC_000014.9:67774535: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 rs117192202

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