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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 Aliases 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.

rs38456

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr7:30538331 (GRCh38.p12) 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>A / T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.17084 (21452/125568, TOPMED)
T=0.1759 (5510/31322, GnomAD)
T=0.214 (1074/5008, 1000G) (+ 5 more)
T=0.204 (915/4480, Estonian)
T=0.184 (711/3854, ALSPAC)
T=0.174 (645/3708, TWINSUK)
T=0.26 (155/600, NorthernSweden)
T=0.17 (36/212, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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.p12 chr 7 NC_000007.14:g.30538331T>A
GRCh38.p12 chr 7 NC_000007.14:g.30538331T>C
GRCh37.p13 chr 7 NC_000007.13:g.30577947T>A
GRCh37.p13 chr 7 NC_000007.13:g.30577947T>C
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
TopMed Global Study-wide 125568 T=0.17084 C=0.82916
gnomAD - Genomes Global Study-wide 31322 T=0.1759 C=0.8241
gnomAD - Genomes European Sub 18852 T=0.1941 C=0.8059
gnomAD - Genomes African Sub 8696 T=0.103 C=0.897
gnomAD - Genomes East Asian Sub 1554 T=0.342 C=0.658
gnomAD - Genomes Other Sub 1084 T=0.205 C=0.795
gnomAD - Genomes American Sub 846 T=0.17 C=0.83
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=0.19 C=0.81
1000Genomes Global Study-wide 5008 T=0.214 C=0.786
1000Genomes African Sub 1322 T=0.088 C=0.912
1000Genomes East Asian Sub 1008 T=0.324 C=0.676
1000Genomes Europe Sub 1006 T=0.185 C=0.815
1000Genomes South Asian Sub 978 T=0.35 C=0.65
1000Genomes American Sub 694 T=0.15 C=0.85
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.204 C=0.796
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.184 C=0.816
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.174 C=0.826
Northern Sweden ACPOP Study-wide 600 T=0.26 C=0.74
A Vietnamese Genetic Variation Database Global Study-wide 212 T=0.17 C=0.83
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= A C Note
GRCh38.p12 chr 7 NC_000007.14:g.30...

NC_000007.14:g.30538331=

NC_000007.14:g.30...

NC_000007.14:g.30538331T>A

NC_000007.14:g.30...

NC_000007.14:g.30538331T>C

GRCh37.p13 chr 7 NC_000007.13:g.30...

NC_000007.13:g.30577947=

NC_000007.13:g.30...

NC_000007.13:g.30577947T>A

NC_000007.13:g.30...

NC_000007.13:g.30577947T>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#.

50 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss43043 May 08, 2000 (76)
2 BCM_SSAHASNP ss10405351 Jul 11, 2003 (116)
3 WI_SSAHASNP ss11894776 Jul 11, 2003 (116)
4 WUGSC_SSAHASNP ss14543168 Dec 05, 2003 (126)
5 SSAHASNP ss22544800 Apr 05, 2004 (123)
6 SSAHASNP ss22921423 Apr 05, 2004 (123)
7 HGSV ss80721636 Dec 16, 2007 (130)
8 HGSV ss85809180 Dec 16, 2007 (130)
9 BCMHGSC_JDW ss93653142 Mar 24, 2008 (129)
10 BUSHMAN ss203137769 Jul 04, 2010 (142)
11 BCM-HGSC-SUB ss208247066 Jul 04, 2010 (142)
12 1000GENOMES ss233911172 Jul 15, 2010 (132)
13 1000GENOMES ss240878742 Jul 15, 2010 (132)
14 BL ss254157920 May 09, 2011 (134)
15 GMI ss279244046 May 04, 2012 (137)
16 GMI ss285598972 Apr 25, 2013 (138)
17 PJP ss294039813 May 09, 2011 (134)
18 TISHKOFF ss559902002 Apr 25, 2013 (138)
19 SSMP ss654255930 Apr 25, 2013 (138)
20 EVA-GONL ss984107694 Aug 21, 2014 (142)
21 JMKIDD_LAB ss1074482968 Aug 21, 2014 (142)
22 1000GENOMES ss1324503581 Aug 21, 2014 (142)
23 DDI ss1431073230 Apr 01, 2015 (144)
24 EVA_GENOME_DK ss1582133563 Apr 01, 2015 (144)
25 EVA_DECODE ss1593678529 Apr 01, 2015 (144)
26 EVA_UK10K_ALSPAC ss1617880216 Apr 01, 2015 (144)
27 EVA_UK10K_TWINSUK ss1660874249 Apr 01, 2015 (144)
28 HAMMER_LAB ss1804935219 Sep 08, 2015 (146)
29 WEILL_CORNELL_DGM ss1927350722 Feb 12, 2016 (147)
30 JJLAB ss2024354631 Sep 14, 2016 (149)
31 USC_VALOUEV ss2152550583 Dec 20, 2016 (150)
32 HUMAN_LONGEVITY ss2292847864 Dec 20, 2016 (150)
33 TOPMED ss2461723419 Dec 20, 2016 (150)
34 SYSTEMSBIOZJU ss2626665572 Nov 08, 2017 (151)
35 GRF ss2708208503 Nov 08, 2017 (151)
36 GNOMAD ss2851376782 Nov 08, 2017 (151)
37 SWEGEN ss3000859403 Nov 08, 2017 (151)
38 BIOINF_KMB_FNS_UNIBA ss3025971664 Nov 08, 2017 (151)
39 CSHL ss3347507396 Nov 08, 2017 (151)
40 TOPMED ss3526202898 Nov 08, 2017 (151)
41 TOPMED ss3526202899 Nov 08, 2017 (151)
42 URBANLAB ss3648594277 Oct 12, 2018 (152)
43 EGCUT_WGS ss3668788363 Jul 13, 2019 (153)
44 EVA_DECODE ss3719383450 Jul 13, 2019 (153)
45 ACPOP ss3734487473 Jul 13, 2019 (153)
46 EVA ss3766366086 Jul 13, 2019 (153)
47 PACBIO ss3785772120 Jul 13, 2019 (153)
48 PACBIO ss3791080939 Jul 13, 2019 (153)
49 PACBIO ss3795960695 Jul 13, 2019 (153)
50 KHV_HUMAN_GENOMES ss3809532092 Jul 13, 2019 (153)
51 1000Genomes NC_000007.13 - 30577947 Oct 12, 2018 (152)
52 The Avon Longitudinal Study of Parents and Children NC_000007.13 - 30577947 Oct 12, 2018 (152)
53 Genetic variation in the Estonian population NC_000007.13 - 30577947 Oct 12, 2018 (152)
54 gnomAD - Genomes NC_000007.13 - 30577947 Jul 13, 2019 (153)
55 Northern Sweden NC_000007.13 - 30577947 Jul 13, 2019 (153)
56 TopMed NC_000007.14 - 30538331 Oct 12, 2018 (152)
57 UK 10K study - Twins NC_000007.13 - 30577947 Oct 12, 2018 (152)
58 A Vietnamese Genetic Variation Database NC_000007.13 - 30577947 Jul 13, 2019 (153)
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)
rs2709780 Mar 10, 2006 (126)
rs10337979 Mar 10, 2006 (126)
rs12701017 Oct 08, 2004 (123)
rs61556202 May 27, 2008 (130)
rs112456408 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3526202898 NC_000007.14:30538330:T:A NC_000007.14:30538330:T:A (self)
ss80721636, ss85809180 NC_000007.11:30351186:T:C NC_000007.14:30538330:T:C (self)
ss93653142, ss203137769, ss208247066, ss254157920, ss279244046, ss285598972, ss294039813, ss1593678529 NC_000007.12:30544471:T:C NC_000007.14:30538330:T:C (self)
36451580, 20324784, 14526611, 99602465, 7772338, 20324784, 4528345, ss233911172, ss240878742, ss559902002, ss654255930, ss984107694, ss1074482968, ss1324503581, ss1431073230, ss1582133563, ss1617880216, ss1660874249, ss1804935219, ss1927350722, ss2024354631, ss2152550583, ss2461723419, ss2626665572, ss2708208503, ss2851376782, ss3000859403, ss3347507396, ss3668788363, ss3734487473, ss3766366086, ss3785772120, ss3791080939, ss3795960695 NC_000007.13:30577946:T:C NC_000007.14:30538330:T:C (self)
361541087, ss2292847864, ss3025971664, ss3526202899, ss3648594277, ss3719383450, ss3809532092 NC_000007.14:30538330:T:C NC_000007.14:30538330:T:C (self)
ss10405351, ss11894776 NT_007819.13:29871554:T:C NC_000007.14:30538330:T:C (self)
ss14543168, ss22544800, ss22921423 NT_007819.14:29871554:T:C NC_000007.14:30538330:T:C (self)
ss43043 NT_007819.17:30567946:T:C NC_000007.14:30538330: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 rs38456

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.post308+0fe9b3b