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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs13007495

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr2:192090779 (GRCh38.p7) 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=0.09306 (11685/125568, TOPMED)
C=0.1109 (3432/30952, GnomAD)
C=0.040 (201/5008, 1000G) (+ 2 more)
C=0.139 (537/3854, ALSPAC)
C=0.145 (536/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TMEFF2 : 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.p7 chr 2 NC_000002.12:g.192090779T>C
GRCh37.p13 chr 2 NC_000002.11:g.192955505T>C
Gene: TMEFF2, transmembrane protein with EGF like and two follistatin like domains 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TMEFF2 transcript variant 2 NM_001305134.1:c. N/A Intron Variant
TMEFF2 transcript variant 1 NM_016192.3:c. N/A Intron Variant
TMEFF2 transcript variant 3 NM_001305145.1:c. N/A Genic Downstream Transcript Variant
TMEFF2 transcript variant X1 XM_011510890.2:c. N/A Intron Variant
TMEFF2 transcript variant X2 XM_017003739.1:c. N/A Intron Variant
TMEFF2 transcript variant X3 XM_017003740.1:c. 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

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
Trans-Omics for Precision Medicine Global Study-wide 125568 T=0.90694 C=0.09306
The Genome Aggregation Database Global Study-wide 30952 T=0.8891 C=0.1109
The Genome Aggregation Database European Sub 18494 T=0.8359 C=0.1641
The Genome Aggregation Database African Sub 8728 T=0.977 C=0.023
The Genome Aggregation Database East Asian Sub 1608 T=0.999 C=0.001
The Genome Aggregation Database Other Sub 982 T=0.88 C=0.12
The Genome Aggregation Database American Sub 838 T=0.93 C=0.07
The Genome Aggregation Database Ashkenazi Jewish Sub 302 T=0.91 C=0.09
1000Genomes Global Study-wide 5008 T=0.960 C=0.040
1000Genomes African Sub 1322 T=0.995 C=0.005
1000Genomes East Asian Sub 1008 T=0.999 C=0.001
1000Genomes Europe Sub 1006 T=0.865 C=0.135
1000Genomes South Asian Sub 978 T=0.97 C=0.03
1000Genomes American Sub 694 T=0.96 C=0.04
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.861 C=0.139
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.855 C=0.145
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 Note
GRCh38.p7 chr 2 NC_000002.12:g.192090779T= NC_000002.12:g.19209077...

NC_000002.12:g.192090779T>C

GRCh37.p13 chr 2 NC_000002.11:g.192955505T= NC_000002.11:g.19295550...

NC_000002.11:g.192955505T>C

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#.

5 Frequency, 57 SubSNP submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss21641276 Apr 05, 2004 (121)
2 PERLEGEN ss24341782 Sep 20, 2004 (123)
3 ABI ss44268726 Mar 15, 2006 (126)
4 AFFY ss66530889 Dec 02, 2006 (127)
5 PERLEGEN ss68838975 May 18, 2007 (127)
6 ILLUMINA ss74965753 Dec 06, 2007 (129)
7 AFFY ss76353449 Dec 06, 2007 (129)
8 KRIBB_YJKIM ss83027686 Dec 16, 2007 (130)
9 HUMANGENOME_JCVI ss97110289 Feb 06, 2009 (130)
10 1000GENOMES ss110496873 Jan 24, 2009 (130)
11 ENSEMBL ss132892061 Dec 01, 2009 (131)
12 COMPLETE_GENOMICS ss167505985 Jul 04, 2010 (132)
13 ILLUMINA ss172302128 Jul 04, 2010 (132)
14 AFFY ss173360831 Jul 04, 2010 (132)
15 BCM-HGSC-SUB ss205825148 Jul 04, 2010 (132)
16 1000GENOMES ss231525424 Jul 14, 2010 (132)
17 EXOME_CHIP ss491329152 May 04, 2012 (137)
18 ILLUMINA ss536827263 Sep 08, 2015 (146)
19 SSMP ss649783888 Apr 25, 2013 (138)
20 ILLUMINA ss780681667 Sep 08, 2015 (146)
21 ILLUMINA ss783354995 Sep 08, 2015 (146)
22 EVA-GONL ss977790475 Aug 21, 2014 (142)
23 JMKIDD_LAB ss1069814564 Aug 21, 2014 (142)
24 1000GENOMES ss1300983247 Aug 21, 2014 (142)
25 HAMMER_LAB ss1397315960 Sep 08, 2015 (146)
26 EVA_GENOME_DK ss1579257743 Apr 01, 2015 (144)
27 EVA_DECODE ss1587237610 Apr 01, 2015 (144)
28 EVA_UK10K_ALSPAC ss1605444689 Apr 01, 2015 (144)
29 EVA_UK10K_TWINSUK ss1648438722 Apr 01, 2015 (144)
30 EVA_SVP ss1712519295 Apr 01, 2015 (144)
31 ILLUMINA ss1752330682 Sep 08, 2015 (146)
32 ILLUMINA ss1917757963 Feb 12, 2016 (147)
33 WEILL_CORNELL_DGM ss1921038570 Feb 12, 2016 (147)
34 ILLUMINA ss1946062234 Feb 12, 2016 (147)
35 ILLUMINA ss1958491352 Feb 12, 2016 (147)
36 JJLAB ss2021060840 Sep 14, 2016 (149)
37 USC_VALOUEV ss2149125756 Dec 20, 2016 (150)
38 HUMAN_LONGEVITY ss2237745771 Dec 20, 2016 (150)
39 TOPMED ss2404182633 Dec 20, 2016 (150)
40 ILLUMINA ss2633720897 Nov 08, 2017 (151)
41 ILLUMINA ss2633720898 Nov 08, 2017 (151)
42 ILLUMINA ss2710921739 Nov 08, 2017 (151)
43 GNOMAD ss2784411046 Nov 08, 2017 (151)
44 AFFY ss2985195561 Nov 08, 2017 (151)
45 AFFY ss2985816679 Nov 08, 2017 (151)
46 SWEGEN ss2991091220 Nov 08, 2017 (151)
47 ILLUMINA ss3022054014 Nov 08, 2017 (151)
48 BIOINF_KMB_FNS_UNIBA ss3024291157 Nov 08, 2017 (151)
49 TOPMED ss3333947084 Nov 08, 2017 (151)
50 CSHL ss3344670107 Nov 08, 2017 (151)
51 ILLUMINA ss3628251718 Jul 19, 2018 (151)
52 ILLUMINA ss3628251719 Jul 19, 2018 (151)
53 ILLUMINA ss3634805121 Jul 19, 2018 (151)
54 ILLUMINA ss3638309621 Jul 19, 2018 (151)
55 ILLUMINA ss3640512420 Jul 19, 2018 (151)
56 ILLUMINA ss3643274961 Jul 19, 2018 (151)
57 ILLUMINA ss3644764903 Jul 19, 2018 (151)
58 1000Genomes NC_000002.11 - 192955505 Jul 19, 2018 (151)
59 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 192955505 Jul 19, 2018 (151)
60 The Genome Aggregation Database NC_000002.11 - 192955505 Jul 19, 2018 (151)
61 Trans-Omics for Precision Medicine NC_000002.12 - 192090779 Jul 19, 2018 (151)
62 UK 10K study - Twins NC_000002.11 - 192955505 Jul 19, 2018 (151)
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)
rs17431895 Oct 07, 2004 (123)
rs61301863 Feb 27, 2009 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss110496873, ss167505985, ss205825148, ss1397315960, ss1587237610, ss1712519295, ss3643274961 NC_000002.10:192663749:T= NC_000002.12:192090778:T= (self)
12062794, 6666486, 113900907, 6666486, ss231525424, ss491329152, ss536827263, ss649783888, ss780681667, ss783354995, ss977790475, ss1069814564, ss1300983247, ss1579257743, ss1605444689, ss1648438722, ss1752330682, ss1917757963, ss1921038570, ss1946062234, ss1958491352, ss2021060840, ss2149125756, ss2404182633, ss2633720897, ss2633720898, ss2710921739, ss2784411046, ss2985195561, ss2985816679, ss2991091220, ss3022054014, ss3344670107, ss3628251718, ss3628251719, ss3634805121, ss3638309621, ss3640512420, ss3644764903 NC_000002.11:192955504:T= NC_000002.12:192090778:T= (self)
213773825, ss2237745771, ss3024291157, ss3333947084 NC_000002.12:192090778:T= NC_000002.12:192090778:T= (self)
ss21641276 NT_005403.14:43164920:T= NC_000002.12:192090778:T= (self)
ss24341782, ss44268726, ss66530889, ss68838975, ss74965753, ss76353449, ss83027686, ss97110289, ss132892061, ss172302128, ss173360831 NT_005403.17:43164922:T= NC_000002.12:192090778:T= (self)
ss110496873, ss167505985, ss205825148, ss1397315960, ss1587237610, ss1712519295, ss3643274961 NC_000002.10:192663749:T>C NC_000002.12:192090778:T>C (self)
12062794, 6666486, 113900907, 6666486, ss231525424, ss491329152, ss536827263, ss649783888, ss780681667, ss783354995, ss977790475, ss1069814564, ss1300983247, ss1579257743, ss1605444689, ss1648438722, ss1752330682, ss1917757963, ss1921038570, ss1946062234, ss1958491352, ss2021060840, ss2149125756, ss2404182633, ss2633720897, ss2633720898, ss2710921739, ss2784411046, ss2985195561, ss2985816679, ss2991091220, ss3022054014, ss3344670107, ss3628251718, ss3628251719, ss3634805121, ss3638309621, ss3640512420, ss3644764903 NC_000002.11:192955504:T>C NC_000002.12:192090778:T>C (self)
213773825, ss2237745771, ss3024291157, ss3333947084 NC_000002.12:192090778:T>C NC_000002.12:192090778:T>C (self)
ss21641276 NT_005403.14:43164920:T>C NC_000002.12:192090778:T>C (self)
ss24341782, ss44268726, ss66530889, ss68838975, ss74965753, ss76353449, ss83027686, ss97110289, ss132892061, ss172302128, ss173360831 NT_005403.17:43164922:T>C NC_000002.12:192090778: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 rs13007495

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: 0.1.4.post833+d3ba21e