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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.

rs142109561

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:89340993 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.001039 (275/264690, TOPMED)
C=0.000207 (52/251456, GnomAD_exome)
C=0.000956 (134/140208, GnomAD) (+ 9 more)
C=0.000231 (28/121366, ExAC)
C=0.000163 (18/110216, ALFA)
C=0.00140 (110/78702, PAGE_STUDY)
C=0.00085 (11/13006, GO-ESP)
C=0.0012 (8/6404, 1000G_30x)
C=0.0010 (5/5008, 1000G)
C=0.0000 (0/3854, ALSPAC)
C=0.0003 (1/3708, TWINSUK)
C=0.002 (1/534, MGP)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
EPHA3 : Missense 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 110216 G=0.999837 C=0.000163
European Sub 92480 G=1.00000 C=0.00000
African Sub 4360 G=0.9963 C=0.0037
African Others Sub 174 G=0.994 C=0.006
African American Sub 4186 G=0.9964 C=0.0036
Asian Sub 3330 G=1.0000 C=0.0000
East Asian Sub 2674 G=1.0000 C=0.0000
Other Asian Sub 656 G=1.000 C=0.000
Latin American 1 Sub 790 G=1.000 C=0.000
Latin American 2 Sub 946 G=1.000 C=0.000
South Asian Sub 274 G=1.000 C=0.000
Other Sub 8036 G=0.9998 C=0.0002


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=0.998961 C=0.001039
gnomAD - Exomes Global Study-wide 251456 G=0.999793 C=0.000207
gnomAD - Exomes European Sub 135384 G=0.999993 C=0.000007
gnomAD - Exomes Asian Sub 49010 G=0.99998 C=0.00002
gnomAD - Exomes American Sub 34590 G=1.00000 C=0.00000
gnomAD - Exomes African Sub 16254 G=0.99692 C=0.00308
gnomAD - Exomes Ashkenazi Jewish Sub 10080 G=1.00000 C=0.00000
gnomAD - Exomes Other Sub 6138 G=1.0000 C=0.0000
gnomAD - Genomes Global Study-wide 140208 G=0.999044 C=0.000956
gnomAD - Genomes European Sub 75946 G=1.00000 C=0.00000
gnomAD - Genomes African Sub 42002 G=0.99688 C=0.00312
gnomAD - Genomes American Sub 13658 G=0.99993 C=0.00007
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3132 G=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2150 G=0.9991 C=0.0009
ExAC Global Study-wide 121366 G=0.999769 C=0.000231
ExAC Europe Sub 73312 G=1.00000 C=0.00000
ExAC Asian Sub 25166 G=1.00000 C=0.00000
ExAC American Sub 11576 G=1.00000 C=0.00000
ExAC African Sub 10404 G=0.99731 C=0.00269
ExAC Other Sub 908 G=1.000 C=0.000
Allele Frequency Aggregator Total Global 110216 G=0.999837 C=0.000163
Allele Frequency Aggregator European Sub 92480 G=1.00000 C=0.00000
Allele Frequency Aggregator Other Sub 8036 G=0.9998 C=0.0002
Allele Frequency Aggregator African Sub 4360 G=0.9963 C=0.0037
Allele Frequency Aggregator Asian Sub 3330 G=1.0000 C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 946 G=1.000 C=0.000
Allele Frequency Aggregator Latin American 1 Sub 790 G=1.000 C=0.000
Allele Frequency Aggregator South Asian Sub 274 G=1.000 C=0.000
The PAGE Study Global Study-wide 78702 G=0.99860 C=0.00140
The PAGE Study AfricanAmerican Sub 32516 G=0.99717 C=0.00283
The PAGE Study Mexican Sub 10810 G=0.99991 C=0.00009
The PAGE Study Asian Sub 8318 G=1.0000 C=0.0000
The PAGE Study PuertoRican Sub 7918 G=0.9994 C=0.0006
The PAGE Study NativeHawaiian Sub 4534 G=1.0000 C=0.0000
The PAGE Study Cuban Sub 4230 G=0.9998 C=0.0002
The PAGE Study Dominican Sub 3828 G=0.9971 C=0.0029
The PAGE Study CentralAmerican Sub 2450 G=1.0000 C=0.0000
The PAGE Study SouthAmerican Sub 1982 G=1.0000 C=0.0000
The PAGE Study NativeAmerican Sub 1260 G=1.0000 C=0.0000
The PAGE Study SouthAsian Sub 856 G=1.000 C=0.000
GO Exome Sequencing Project Global Study-wide 13006 G=0.99915 C=0.00085
GO Exome Sequencing Project European American Sub 8600 G=1.0000 C=0.0000
GO Exome Sequencing Project African American Sub 4406 G=0.9975 C=0.0025
1000Genomes_30x Global Study-wide 6404 G=0.9988 C=0.0012
1000Genomes_30x African Sub 1786 G=0.9955 C=0.0045
1000Genomes_30x Europe Sub 1266 G=1.0000 C=0.0000
1000Genomes_30x South Asian Sub 1202 G=1.0000 C=0.0000
1000Genomes_30x East Asian Sub 1170 G=1.0000 C=0.0000
1000Genomes_30x American Sub 980 G=1.000 C=0.000
1000Genomes Global Study-wide 5008 G=0.9990 C=0.0010
1000Genomes African Sub 1322 G=0.9962 C=0.0038
1000Genomes East Asian Sub 1008 G=1.0000 C=0.0000
1000Genomes Europe Sub 1006 G=1.0000 C=0.0000
1000Genomes South Asian Sub 978 G=1.000 C=0.000
1000Genomes American Sub 694 G=1.000 C=0.000
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=1.0000 C=0.0000
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9997 C=0.0003
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.998 C=0.002
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 3 NC_000003.12:g.89340993G>C
GRCh37.p13 chr 3 NC_000003.11:g.89390143G>C
EPHA3 RefSeqGene NG_023239.2:g.238470G>C
Gene: EPHA3, EPH receptor A3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
EPHA3 transcript variant 1 NM_005233.6:c.892G>C E [GAA] > Q [CAA] Coding Sequence Variant
ephrin type-A receptor 3 isoform a precursor NP_005224.2:p.Glu298Gln E (Glu) > Q (Gln) Missense Variant
EPHA3 transcript variant 2 NM_182644.3:c.892G>C E [GAA] > Q [CAA] Coding Sequence Variant
ephrin type-A receptor 3 isoform b precursor NP_872585.1:p.Glu298Gln E (Glu) > Q (Gln) Missense Variant
EPHA3 transcript variant X1 XM_005264715.4:c.892G>C E [GAA] > Q [CAA] Coding Sequence Variant
ephrin type-A receptor 3 isoform X1 XP_005264772.1:p.Glu298Gln E (Glu) > Q (Gln) Missense Variant
EPHA3 transcript variant X2 XM_005264716.4:c.892G>C E [GAA] > Q [CAA] Coding Sequence Variant
ephrin type-A receptor 3 isoform X2 XP_005264773.1:p.Glu298Gln E (Glu) > Q (Gln) Missense Variant
EPHA3 transcript variant X2 XM_047447673.1:c.892G>C E [GAA] > Q [CAA] Coding Sequence Variant
ephrin type-A receptor 3 isoform X2 XP_047303629.1:p.Glu298Gln E (Glu) > Q (Gln) Missense 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= C
GRCh38.p14 chr 3 NC_000003.12:g.89340993= NC_000003.12:g.89340993G>C
GRCh37.p13 chr 3 NC_000003.11:g.89390143= NC_000003.11:g.89390143G>C
EPHA3 RefSeqGene NG_023239.2:g.238470= NG_023239.2:g.238470G>C
EPHA3 transcript variant 1 NM_005233.6:c.892= NM_005233.6:c.892G>C
EPHA3 transcript variant 1 NM_005233.5:c.892= NM_005233.5:c.892G>C
EPHA3 transcript variant 2 NM_182644.3:c.892= NM_182644.3:c.892G>C
EPHA3 transcript variant 2 NM_182644.2:c.892= NM_182644.2:c.892G>C
EPHA3 transcript variant X1 XM_005264715.4:c.892= XM_005264715.4:c.892G>C
EPHA3 transcript variant X1 XM_005264715.3:c.892= XM_005264715.3:c.892G>C
EPHA3 transcript variant X1 XM_005264715.2:c.892= XM_005264715.2:c.892G>C
EPHA3 transcript variant X1 XM_005264715.1:c.892= XM_005264715.1:c.892G>C
EPHA3 transcript variant X2 XM_005264716.4:c.892= XM_005264716.4:c.892G>C
EPHA3 transcript variant 3 NM_001410778.1:c.892= NM_001410778.1:c.892G>C
EPHA3 transcript variant X2 XM_047447673.1:c.892= XM_047447673.1:c.892G>C
ephrin type-A receptor 3 isoform a precursor NP_005224.2:p.Glu298= NP_005224.2:p.Glu298Gln
ephrin type-A receptor 3 isoform b precursor NP_872585.1:p.Glu298= NP_872585.1:p.Glu298Gln
ephrin type-A receptor 3 isoform X1 XP_005264772.1:p.Glu298= XP_005264772.1:p.Glu298Gln
ephrin type-A receptor 3 isoform X2 XP_005264773.1:p.Glu298= XP_005264773.1:p.Glu298Gln
ephrin type-A receptor 3 isoform X2 XP_047303629.1:p.Glu298= XP_047303629.1:p.Glu298Gln
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#.

41 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342140037 May 09, 2011 (134)
2 EXOME_CHIP ss491342749 May 04, 2012 (137)
3 ILLUMINA ss780819185 Sep 08, 2015 (146)
4 ILLUMINA ss783501548 Sep 08, 2015 (146)
5 1000GENOMES ss1305064714 Aug 21, 2014 (142)
6 EVA_UK10K_ALSPAC ss1607635266 Apr 01, 2015 (144)
7 EVA_UK10K_TWINSUK ss1650629299 Apr 01, 2015 (144)
8 EVA_EXAC ss1687105047 Apr 01, 2015 (144)
9 EVA_MGP ss1711024894 Apr 01, 2015 (144)
10 ILLUMINA ss1752486964 Sep 08, 2015 (146)
11 ILLUMINA ss1917769689 Feb 12, 2016 (147)
12 ILLUMINA ss1946089059 Feb 12, 2016 (147)
13 ILLUMINA ss1958585246 Feb 12, 2016 (147)
14 GNOMAD ss2733907431 Nov 08, 2017 (151)
15 GNOMAD ss2747053274 Nov 08, 2017 (151)
16 GNOMAD ss2795994329 Nov 08, 2017 (151)
17 AFFY ss2985263050 Nov 08, 2017 (151)
18 AFFY ss2985884707 Nov 08, 2017 (151)
19 ILLUMINA ss3022263544 Nov 08, 2017 (151)
20 ILLUMINA ss3625820820 Oct 12, 2018 (152)
21 ILLUMINA ss3628718281 Oct 12, 2018 (152)
22 ILLUMINA ss3634905826 Oct 12, 2018 (152)
23 ILLUMINA ss3640613127 Oct 12, 2018 (152)
24 ILLUMINA ss3644821671 Oct 12, 2018 (152)
25 ILLUMINA ss3652740459 Oct 12, 2018 (152)
26 ILLUMINA ss3654031911 Oct 12, 2018 (152)
27 ILLUMINA ss3726036111 Jul 13, 2019 (153)
28 ILLUMINA ss3744512949 Jul 13, 2019 (153)
29 ILLUMINA ss3745205811 Jul 13, 2019 (153)
30 PAGE_CC ss3771047842 Jul 13, 2019 (153)
31 ILLUMINA ss3772701163 Jul 13, 2019 (153)
32 EVA ss3823934227 Apr 25, 2020 (154)
33 EVA ss3986246106 Apr 26, 2021 (155)
34 TOPMED ss4574030931 Apr 26, 2021 (155)
35 1000G_HIGH_COVERAGE ss5255011734 Oct 12, 2022 (156)
36 EVA ss5341538183 Oct 12, 2022 (156)
37 HUGCELL_USP ss5454310131 Oct 12, 2022 (156)
38 1000G_HIGH_COVERAGE ss5533893321 Oct 12, 2022 (156)
39 EVA ss5847973208 Oct 12, 2022 (156)
40 EVA ss5869899030 Oct 12, 2022 (156)
41 EVA ss5960973008 Oct 12, 2022 (156)
42 1000Genomes NC_000003.11 - 89390143 Oct 12, 2018 (152)
43 1000Genomes_30x NC_000003.12 - 89340993 Oct 12, 2022 (156)
44 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 89390143 Oct 12, 2018 (152)
45 ExAC NC_000003.11 - 89390143 Oct 12, 2018 (152)
46 gnomAD - Genomes NC_000003.12 - 89340993 Apr 26, 2021 (155)
47 gnomAD - Exomes NC_000003.11 - 89390143 Jul 13, 2019 (153)
48 GO Exome Sequencing Project NC_000003.11 - 89390143 Oct 12, 2018 (152)
49 Medical Genome Project healthy controls from Spanish population NC_000003.11 - 89390143 Apr 25, 2020 (154)
50 The PAGE Study NC_000003.12 - 89340993 Jul 13, 2019 (153)
51 TopMed NC_000003.12 - 89340993 Apr 26, 2021 (155)
52 UK 10K study - Twins NC_000003.11 - 89390143 Oct 12, 2018 (152)
53 ALFA NC_000003.12 - 89340993 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
16288654, 9067232, 7036467, 2989354, 392537, 141106, 9067232, ss342140037, ss491342749, ss780819185, ss783501548, ss1305064714, ss1607635266, ss1650629299, ss1687105047, ss1711024894, ss1752486964, ss1917769689, ss1946089059, ss1958585246, ss2733907431, ss2747053274, ss2795994329, ss2985263050, ss2985884707, ss3022263544, ss3625820820, ss3628718281, ss3634905826, ss3640613127, ss3644821671, ss3652740459, ss3654031911, ss3744512949, ss3745205811, ss3772701163, ss3823934227, ss3986246106, ss5341538183, ss5847973208, ss5960973008 NC_000003.11:89390142:G:C NC_000003.12:89340992:G:C (self)
21419256, 115668114, 269311, 411408486, 13078886444, ss3726036111, ss3771047842, ss4574030931, ss5255011734, ss5454310131, ss5533893321, ss5869899030 NC_000003.12:89340992:G:C NC_000003.12:89340992:G: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 rs142109561

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