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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.

rs17082122

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:65415228 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.144195 (38167/264690, TOPMED)
C=0.140966 (19744/140062, GnomAD)
C=0.27897 (7883/28258, 14KJPN) (+ 19 more)
C=0.17630 (4531/25700, ALFA)
C=0.28341 (4750/16760, 8.3KJPN)
C=0.1780 (1140/6404, 1000G_30x)
C=0.1823 (913/5008, 1000G)
C=0.2406 (1078/4480, Estonian)
C=0.1424 (549/3854, ALSPAC)
C=0.1478 (548/3708, TWINSUK)
C=0.2853 (836/2930, KOREAN)
C=0.2849 (522/1832, Korea1K)
C=0.1525 (272/1784, HapMap)
C=0.138 (138/998, GoNL)
C=0.379 (237/626, Chileans)
C=0.202 (121/600, NorthernSweden)
C=0.106 (23/216, Qatari)
C=0.283 (60/212, Vietnamese)
T=0.320 (66/206, SGDP_PRJ)
C=0.12 (5/40, GENOME_DK)
T=0.50 (13/26, Siberian)
C=0.50 (13/26, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
EPHA5 : 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 25700 T=0.82370 C=0.17630
European Sub 17398 T=0.82113 C=0.17887
African Sub 3624 T=0.9622 C=0.0378
African Others Sub 126 T=0.992 C=0.008
African American Sub 3498 T=0.9611 C=0.0389
Asian Sub 160 T=0.694 C=0.306
East Asian Sub 102 T=0.716 C=0.284
Other Asian Sub 58 T=0.66 C=0.34
Latin American 1 Sub 292 T=0.839 C=0.161
Latin American 2 Sub 2770 T=0.6830 C=0.3170
South Asian Sub 110 T=0.827 C=0.173
Other Sub 1346 T=0.7853 C=0.2147


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 T=0.855805 C=0.144195
gnomAD - Genomes Global Study-wide 140062 T=0.859034 C=0.140966
gnomAD - Genomes European Sub 75830 T=0.83074 C=0.16926
gnomAD - Genomes African Sub 42018 T=0.95880 C=0.04120
gnomAD - Genomes American Sub 13620 T=0.75235 C=0.24765
gnomAD - Genomes Ashkenazi Jewish Sub 3320 T=0.8316 C=0.1684
gnomAD - Genomes East Asian Sub 3126 T=0.7028 C=0.2972
gnomAD - Genomes Other Sub 2148 T=0.8524 C=0.1476
14KJPN JAPANESE Study-wide 28258 T=0.72103 C=0.27897
Allele Frequency Aggregator Total Global 25700 T=0.82370 C=0.17630
Allele Frequency Aggregator European Sub 17398 T=0.82113 C=0.17887
Allele Frequency Aggregator African Sub 3624 T=0.9622 C=0.0378
Allele Frequency Aggregator Latin American 2 Sub 2770 T=0.6830 C=0.3170
Allele Frequency Aggregator Other Sub 1346 T=0.7853 C=0.2147
Allele Frequency Aggregator Latin American 1 Sub 292 T=0.839 C=0.161
Allele Frequency Aggregator Asian Sub 160 T=0.694 C=0.306
Allele Frequency Aggregator South Asian Sub 110 T=0.827 C=0.173
8.3KJPN JAPANESE Study-wide 16760 T=0.71659 C=0.28341
1000Genomes_30x Global Study-wide 6404 T=0.8220 C=0.1780
1000Genomes_30x African Sub 1786 T=0.9849 C=0.0151
1000Genomes_30x Europe Sub 1266 T=0.8278 C=0.1722
1000Genomes_30x South Asian Sub 1202 T=0.7829 C=0.2171
1000Genomes_30x East Asian Sub 1170 T=0.7154 C=0.2846
1000Genomes_30x American Sub 980 T=0.693 C=0.307
1000Genomes Global Study-wide 5008 T=0.8177 C=0.1823
1000Genomes African Sub 1322 T=0.9841 C=0.0159
1000Genomes East Asian Sub 1008 T=0.7143 C=0.2857
1000Genomes Europe Sub 1006 T=0.8280 C=0.1720
1000Genomes South Asian Sub 978 T=0.773 C=0.227
1000Genomes American Sub 694 T=0.699 C=0.301
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.7594 C=0.2406
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.8576 C=0.1424
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.8522 C=0.1478
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.7147 C=0.2853
Korean Genome Project KOREAN Study-wide 1832 T=0.7151 C=0.2849
HapMap Global Study-wide 1784 T=0.8475 C=0.1525
HapMap American Sub 768 T=0.770 C=0.230
HapMap African Sub 586 T=0.985 C=0.015
HapMap Asian Sub 254 T=0.732 C=0.268
HapMap Europe Sub 176 T=0.898 C=0.102
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.862 C=0.138
Chileans Chilean Study-wide 626 T=0.621 C=0.379
Northern Sweden ACPOP Study-wide 600 T=0.798 C=0.202
Qatari Global Study-wide 216 T=0.894 C=0.106
A Vietnamese Genetic Variation Database Global Study-wide 212 T=0.717 C=0.283
SGDP_PRJ Global Study-wide 206 T=0.320 C=0.680
The Danish reference pan genome Danish Study-wide 40 T=0.88 C=0.12
Siberian Global Study-wide 26 T=0.50 C=0.50
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 4 NC_000004.12:g.65415228T>C
GRCh37.p13 chr 4 NC_000004.11:g.66280946T>C
Gene: EPHA5, EPH receptor A5 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
EPHA5 transcript variant 3 NM_001281765.3:c.1528-785…

NM_001281765.3:c.1528-785A>G

N/A Intron Variant
EPHA5 transcript variant 4 NM_001281766.3:c.1528-785…

NM_001281766.3:c.1528-785A>G

N/A Intron Variant
EPHA5 transcript variant 5 NM_001281767.3:c.1528-785…

NM_001281767.3:c.1528-785A>G

N/A Intron Variant
EPHA5 transcript variant 6 NM_001318761.2:c.1321-785…

NM_001318761.2:c.1321-785A>G

N/A Intron Variant
EPHA5 transcript variant 1 NM_004439.8:c.1528-785A>G N/A Intron Variant
EPHA5 transcript variant 2 NM_182472.5:c.1528-785A>G N/A Intron Variant
EPHA5 transcript variant X4 XM_005265653.5:c.1036-785…

XM_005265653.5:c.1036-785A>G

N/A Intron Variant
EPHA5 transcript variant X1 XM_011531735.4:c.1192-785…

XM_011531735.4:c.1192-785A>G

N/A Intron Variant
EPHA5 transcript variant X2 XM_017007878.3:c.1192-785…

XM_017007878.3:c.1192-785A>G

N/A Intron Variant
EPHA5 transcript variant X6 XM_017007880.3:c.1036-785…

XM_017007880.3:c.1036-785A>G

N/A Intron Variant
EPHA5 transcript variant X7 XM_017007881.3:c.1036-785…

XM_017007881.3:c.1036-785A>G

N/A Intron Variant
EPHA5 transcript variant X3 XM_047449762.1:c.1192-785…

XM_047449762.1:c.1192-785A>G

N/A Intron Variant
EPHA5 transcript variant X5 XM_047449763.1:c.1036-785…

XM_047449763.1:c.1036-785A>G

N/A Intron 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 T= C
GRCh38.p14 chr 4 NC_000004.12:g.65415228= NC_000004.12:g.65415228T>C
GRCh37.p13 chr 4 NC_000004.11:g.66280946= NC_000004.11:g.66280946T>C
EPHA5 transcript variant 3 NM_001281765.3:c.1528-785= NM_001281765.3:c.1528-785A>G
EPHA5 transcript variant 4 NM_001281766.3:c.1528-785= NM_001281766.3:c.1528-785A>G
EPHA5 transcript variant 5 NM_001281767.3:c.1528-785= NM_001281767.3:c.1528-785A>G
EPHA5 transcript variant 6 NM_001318761.2:c.1321-785= NM_001318761.2:c.1321-785A>G
EPHA5 transcript variant 1 NM_004439.5:c.1528-785= NM_004439.5:c.1528-785A>G
EPHA5 transcript variant 1 NM_004439.8:c.1528-785= NM_004439.8:c.1528-785A>G
EPHA5 transcript variant 2 NM_182472.2:c.1528-785= NM_182472.2:c.1528-785A>G
EPHA5 transcript variant 2 NM_182472.5:c.1528-785= NM_182472.5:c.1528-785A>G
EPHA5 transcript variant X1 XM_005265650.1:c.1528-785= XM_005265650.1:c.1528-785A>G
EPHA5 transcript variant X2 XM_005265651.1:c.1528-785= XM_005265651.1:c.1528-785A>G
EPHA5 transcript variant X3 XM_005265652.1:c.1321-785= XM_005265652.1:c.1321-785A>G
EPHA5 transcript variant X4 XM_005265653.1:c.1036-785= XM_005265653.1:c.1036-785A>G
EPHA5 transcript variant X4 XM_005265653.5:c.1036-785= XM_005265653.5:c.1036-785A>G
EPHA5 transcript variant X1 XM_011531735.4:c.1192-785= XM_011531735.4:c.1192-785A>G
EPHA5 transcript variant X2 XM_017007878.3:c.1192-785= XM_017007878.3:c.1192-785A>G
EPHA5 transcript variant X6 XM_017007880.3:c.1036-785= XM_017007880.3:c.1036-785A>G
EPHA5 transcript variant X7 XM_017007881.3:c.1036-785= XM_017007881.3:c.1036-785A>G
EPHA5 transcript variant X3 XM_047449762.1:c.1192-785= XM_047449762.1:c.1192-785A>G
EPHA5 transcript variant X5 XM_047449763.1:c.1036-785= XM_047449763.1:c.1036-785A>G
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#.

64 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss23880835 Sep 20, 2004 (123)
2 AFFY ss66036225 Jul 04, 2010 (132)
3 PERLEGEN ss68900908 May 17, 2007 (127)
4 AFFY ss75924933 Dec 07, 2007 (129)
5 KRIBB_YJKIM ss83182177 Dec 14, 2007 (130)
6 HUMANGENOME_JCVI ss98966391 Feb 06, 2009 (130)
7 BGI ss104076275 Dec 01, 2009 (131)
8 1000GENOMES ss107995592 Jan 22, 2009 (130)
9 ENSEMBL ss143060350 Dec 01, 2009 (131)
10 GMI ss157367629 Dec 01, 2009 (131)
11 AFFY ss169199653 Jul 04, 2010 (132)
12 BUSHMAN ss198617728 Jul 04, 2010 (132)
13 1000GENOMES ss232421405 Jul 14, 2010 (132)
14 1000GENOMES ss239708814 Jul 15, 2010 (132)
15 GMI ss277750619 May 04, 2012 (137)
16 SSMP ss651365884 Apr 25, 2013 (138)
17 EVA-GONL ss980189498 Aug 21, 2014 (142)
18 JMKIDD_LAB ss1071594193 Aug 21, 2014 (142)
19 1000GENOMES ss1310021531 Aug 21, 2014 (142)
20 EVA_GENOME_DK ss1580587576 Apr 01, 2015 (144)
21 EVA_DECODE ss1589690771 Apr 01, 2015 (144)
22 EVA_UK10K_ALSPAC ss1610228490 Apr 01, 2015 (144)
23 EVA_UK10K_TWINSUK ss1653222523 Apr 01, 2015 (144)
24 EVA_SVP ss1712677168 Apr 01, 2015 (144)
25 WEILL_CORNELL_DGM ss1923431055 Feb 12, 2016 (147)
26 GENOMED ss1969758789 Jul 19, 2016 (147)
27 JJLAB ss2022301194 Sep 14, 2016 (149)
28 USC_VALOUEV ss2150426955 Dec 20, 2016 (150)
29 HUMAN_LONGEVITY ss2263469967 Dec 20, 2016 (150)
30 SYSTEMSBIOZJU ss2625649466 Nov 08, 2017 (151)
31 GRF ss2705896923 Nov 08, 2017 (151)
32 GNOMAD ss2810110760 Nov 08, 2017 (151)
33 SWEGEN ss2994816501 Nov 08, 2017 (151)
34 BIOINF_KMB_FNS_UNIBA ss3024923102 Nov 08, 2017 (151)
35 CSHL ss3345750638 Nov 08, 2017 (151)
36 URBANLAB ss3647747735 Oct 12, 2018 (152)
37 EGCUT_WGS ss3662707964 Jul 13, 2019 (153)
38 EVA_DECODE ss3712189813 Jul 13, 2019 (153)
39 ACPOP ss3731213225 Jul 13, 2019 (153)
40 EVA ss3761883511 Jul 13, 2019 (153)
41 PACBIO ss3784733596 Jul 13, 2019 (153)
42 PACBIO ss3790189010 Jul 13, 2019 (153)
43 PACBIO ss3795064108 Jul 13, 2019 (153)
44 KHV_HUMAN_GENOMES ss3805023208 Jul 13, 2019 (153)
45 EVA ss3828578661 Apr 26, 2020 (154)
46 EVA ss3837728476 Apr 26, 2020 (154)
47 EVA ss3843165250 Apr 26, 2020 (154)
48 SGDP_PRJ ss3859102669 Apr 26, 2020 (154)
49 KRGDB ss3905348352 Apr 26, 2020 (154)
50 KOGIC ss3954315796 Apr 26, 2020 (154)
51 TOPMED ss4616295134 Apr 26, 2021 (155)
52 TOMMO_GENOMICS ss5166030590 Apr 26, 2021 (155)
53 1000G_HIGH_COVERAGE ss5259453929 Oct 17, 2022 (156)
54 EVA ss5349460219 Oct 17, 2022 (156)
55 HUGCELL_USP ss5458185582 Oct 17, 2022 (156)
56 EVA ss5507543392 Oct 17, 2022 (156)
57 1000G_HIGH_COVERAGE ss5540667901 Oct 17, 2022 (156)
58 SANFORD_IMAGENETICS ss5635179208 Oct 17, 2022 (156)
59 TOMMO_GENOMICS ss5700462037 Oct 17, 2022 (156)
60 YY_MCH ss5805147462 Oct 17, 2022 (156)
61 EVA ss5844094533 Oct 17, 2022 (156)
62 EVA ss5854253633 Oct 17, 2022 (156)
63 EVA ss5863722857 Oct 17, 2022 (156)
64 EVA ss5963552395 Oct 17, 2022 (156)
65 1000Genomes NC_000004.11 - 66280946 Oct 12, 2018 (152)
66 1000Genomes_30x NC_000004.12 - 65415228 Oct 17, 2022 (156)
67 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 66280946 Oct 12, 2018 (152)
68 Chileans NC_000004.11 - 66280946 Apr 26, 2020 (154)
69 Genetic variation in the Estonian population NC_000004.11 - 66280946 Oct 12, 2018 (152)
70 The Danish reference pan genome NC_000004.11 - 66280946 Apr 26, 2020 (154)
71 gnomAD - Genomes NC_000004.12 - 65415228 Apr 26, 2021 (155)
72 Genome of the Netherlands Release 5 NC_000004.11 - 66280946 Apr 26, 2020 (154)
73 HapMap NC_000004.12 - 65415228 Apr 26, 2020 (154)
74 KOREAN population from KRGDB NC_000004.11 - 66280946 Apr 26, 2020 (154)
75 Korean Genome Project NC_000004.12 - 65415228 Apr 26, 2020 (154)
76 Northern Sweden NC_000004.11 - 66280946 Jul 13, 2019 (153)
77 Qatari NC_000004.11 - 66280946 Apr 26, 2020 (154)
78 SGDP_PRJ NC_000004.11 - 66280946 Apr 26, 2020 (154)
79 Siberian NC_000004.11 - 66280946 Apr 26, 2020 (154)
80 8.3KJPN NC_000004.11 - 66280946 Apr 26, 2021 (155)
81 14KJPN NC_000004.12 - 65415228 Oct 17, 2022 (156)
82 TopMed NC_000004.12 - 65415228 Apr 26, 2021 (155)
83 UK 10K study - Twins NC_000004.11 - 66280946 Oct 12, 2018 (152)
84 A Vietnamese Genetic Variation Database NC_000004.11 - 66280946 Jul 13, 2019 (153)
85 ALFA NC_000004.12 - 65415228 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)
rs58030593 Feb 27, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss75924933, ss107995592, ss169199653, ss198617728, ss277750619, ss1589690771, ss1712677168 NC_000004.10:65963540:T:C NC_000004.12:65415227:T:C (self)
21426976, 11915454, 317474, 8446212, 6752515, 5259312, 12525746, 4498090, 5472985, 11119649, 2943309, 23999897, 11915454, 2622061, ss232421405, ss239708814, ss651365884, ss980189498, ss1071594193, ss1310021531, ss1580587576, ss1610228490, ss1653222523, ss1923431055, ss1969758789, ss2022301194, ss2150426955, ss2625649466, ss2705896923, ss2810110760, ss2994816501, ss3345750638, ss3662707964, ss3731213225, ss3761883511, ss3784733596, ss3790189010, ss3795064108, ss3828578661, ss3837728476, ss3859102669, ss3905348352, ss5166030590, ss5349460219, ss5507543392, ss5635179208, ss5844094533, ss5963552395 NC_000004.11:66280945:T:C NC_000004.12:65415227:T:C (self)
28193836, 151834359, 2627446, 10693797, 34299141, 453672690, 2474888225, ss2263469967, ss3024923102, ss3647747735, ss3712189813, ss3805023208, ss3843165250, ss3954315796, ss4616295134, ss5259453929, ss5458185582, ss5540667901, ss5700462037, ss5805147462, ss5854253633, ss5863722857 NC_000004.12:65415227:T:C NC_000004.12:65415227:T:C (self)
ss66036225 NT_016354.20:6493846:T:C NC_000004.12:65415227:T:C (self)
ss23880835, ss68900908, ss83182177, ss98966391, ss104076275, ss143060350, ss157367629 NT_022778.16:6491612:T:C NC_000004.12:65415227:T: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 rs17082122

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