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dbSNP Short Genetic Variations

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.

rs2541505

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr16:10670715 (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
A>C / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.32322 (40586/125568, TOPMED)
C=0.3025 (9475/31324, GnomAD)
C=0.420 (2105/5008, 1000G) (+ 5 more)
C=0.208 (933/4480, Estonian)
C=0.192 (740/3854, ALSPAC)
C=0.184 (681/3708, TWINSUK)
C=0.19 (116/600, NorthernSweden)
C=0.47 (101/216, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TEKT5 : 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.p12 chr 16 NC_000016.10:g.10670715A>C
GRCh38.p12 chr 16 NC_000016.10:g.10670715A>T
GRCh37.p13 chr 16 NC_000016.9:g.10764572A>C
GRCh37.p13 chr 16 NC_000016.9:g.10764572A>T
Gene: TEKT5, tektin 5 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TEKT5 transcript NM_144674.2: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
TopMed Global Study-wide 125568 A=0.67678 C=0.32322
gnomAD - Genomes Global Study-wide 31324 A=0.6975 C=0.3025
gnomAD - Genomes European Sub 18872 A=0.8042 C=0.1958
gnomAD - Genomes African Sub 8684 A=0.521 C=0.479
gnomAD - Genomes East Asian Sub 1548 A=0.426 C=0.574
gnomAD - Genomes Other Sub 1084 A=0.756 C=0.244
gnomAD - Genomes American Sub 846 A=0.51 C=0.49
gnomAD - Genomes Ashkenazi Jewish Sub 290 A=0.81 C=0.19
1000Genomes Global Study-wide 5008 A=0.580 C=0.420
1000Genomes African Sub 1322 A=0.489 C=0.511
1000Genomes East Asian Sub 1008 A=0.438 C=0.562
1000Genomes Europe Sub 1006 A=0.820 C=0.180
1000Genomes South Asian Sub 978 A=0.61 C=0.39
1000Genomes American Sub 694 A=0.57 C=0.43
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.792 C=0.208
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.808 C=0.192
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.816 C=0.184
Northern Sweden ACPOP Study-wide 600 A=0.81 C=0.19
A Vietnamese Genetic Variation Database Global Study-wide 216 A=0.53 C=0.47
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 A= C T Note
GRCh38.p12 chr 16 NC_000016.10:g.10...

NC_000016.10:g.10670715=

NC_000016.10:g.10...

NC_000016.10:g.10670715A>C

NC_000016.10:g.10...

NC_000016.10:g.10670715A>T

GRCh37.p13 chr 16 NC_000016.9:g.107...

NC_000016.9:g.10764572=

NC_000016.9:g.107...

NC_000016.9:g.10764572A>C

NC_000016.9:g.107...

NC_000016.9:g.10764572A>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#.

52 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3562843 Sep 28, 2001 (100)
2 BCM_SSAHASNP ss14257530 Dec 05, 2003 (119)
3 ABI ss43899020 Mar 13, 2006 (126)
4 HGSV ss83394324 Dec 14, 2007 (130)
5 BCMHGSC_JDW ss90319445 Mar 24, 2008 (129)
6 BGI ss106461664 Feb 04, 2009 (130)
7 1000GENOMES ss109199708 Jan 23, 2009 (130)
8 1000GENOMES ss114851261 Jan 25, 2009 (130)
9 ENSEMBL ss136592490 Dec 01, 2009 (131)
10 COMPLETE_GENOMICS ss169176579 Jul 04, 2010 (132)
11 BUSHMAN ss201448843 Jul 04, 2010 (132)
12 1000GENOMES ss227147486 Jul 14, 2010 (132)
13 1000GENOMES ss236956518 Jul 15, 2010 (132)
14 1000GENOMES ss243309871 Jul 15, 2010 (132)
15 BL ss255515159 May 09, 2011 (134)
16 GMI ss282439961 May 04, 2012 (137)
17 GMI ss287036214 Apr 25, 2013 (138)
18 PJP ss291920300 May 09, 2011 (134)
19 TISHKOFF ss564786844 Apr 25, 2013 (138)
20 SSMP ss660531390 Apr 25, 2013 (138)
21 EVA-GONL ss992290137 Aug 21, 2014 (142)
22 JMKIDD_LAB ss1080492569 Aug 21, 2014 (142)
23 1000GENOMES ss1355411779 Aug 21, 2014 (142)
24 DDI ss1427781756 Apr 01, 2015 (144)
25 EVA_GENOME_DK ss1577839225 Apr 01, 2015 (144)
26 EVA_UK10K_ALSPAC ss1634025359 Apr 01, 2015 (144)
27 EVA_UK10K_TWINSUK ss1677019392 Apr 01, 2015 (144)
28 EVA_DECODE ss1696325976 Apr 01, 2015 (144)
29 HAMMER_LAB ss1808426323 Sep 08, 2015 (146)
30 WEILL_CORNELL_DGM ss1935705853 Feb 12, 2016 (147)
31 GENOMED ss1968222795 Jul 19, 2016 (147)
32 JJLAB ss2028639661 Sep 14, 2016 (149)
33 USC_VALOUEV ss2157050857 Dec 20, 2016 (150)
34 HUMAN_LONGEVITY ss2210679165 Dec 20, 2016 (150)
35 TOPMED ss2375324066 Dec 20, 2016 (150)
36 SYSTEMSBIOZJU ss2628814191 Nov 08, 2017 (151)
37 GRF ss2701546447 Nov 08, 2017 (151)
38 GNOMAD ss2940382364 Nov 08, 2017 (151)
39 SWEGEN ss3014076782 Nov 08, 2017 (151)
40 BIOINF_KMB_FNS_UNIBA ss3028145662 Nov 08, 2017 (151)
41 TOPMED ss3240225871 Nov 08, 2017 (151)
42 TOPMED ss3240225872 Nov 08, 2017 (151)
43 CSHL ss3351341332 Nov 08, 2017 (151)
44 URBANLAB ss3650465189 Oct 12, 2018 (152)
45 EGCUT_WGS ss3681199820 Jul 13, 2019 (153)
46 EVA_DECODE ss3698853687 Jul 13, 2019 (153)
47 ACPOP ss3741342688 Jul 13, 2019 (153)
48 EVA ss3753695372 Jul 13, 2019 (153)
49 PACBIO ss3787982706 Jul 13, 2019 (153)
50 PACBIO ss3792975563 Jul 13, 2019 (153)
51 PACBIO ss3797860523 Jul 13, 2019 (153)
52 KHV_HUMAN_GENOMES ss3818992031 Jul 13, 2019 (153)
53 1000Genomes NC_000016.9 - 10764572 Oct 12, 2018 (152)
54 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 10764572 Oct 12, 2018 (152)
55 Genetic variation in the Estonian population NC_000016.9 - 10764572 Oct 12, 2018 (152)
56 gnomAD - Genomes NC_000016.9 - 10764572 Jul 13, 2019 (153)
57 Northern Sweden NC_000016.9 - 10764572 Jul 13, 2019 (153)
58 TopMed NC_000016.10 - 10670715 Oct 12, 2018 (152)
59 UK 10K study - Twins NC_000016.9 - 10764572 Oct 12, 2018 (152)
60 A Vietnamese Genetic Variation Database NC_000016.9 - 10764572 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)
rs57482047 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss83394324, ss90319445, ss109199708, ss114851261, ss169176579, ss201448843, ss255515159, ss282439961, ss287036214, ss291920300, ss1696325976 NC_000016.8:10672072:A:C NC_000016.10:10670714:A:C (self)
68547640, 38060921, 26938068, 187025956, 14627553, 38060921, 8457981, ss227147486, ss236956518, ss243309871, ss564786844, ss660531390, ss992290137, ss1080492569, ss1355411779, ss1427781756, ss1577839225, ss1634025359, ss1677019392, ss1808426323, ss1935705853, ss1968222795, ss2028639661, ss2157050857, ss2375324066, ss2628814191, ss2701546447, ss2940382364, ss3014076782, ss3351341332, ss3681199820, ss3741342688, ss3753695372, ss3787982706, ss3792975563, ss3797860523 NC_000016.9:10764571:A:C NC_000016.10:10670714:A:C (self)
139740018, ss2210679165, ss3028145662, ss3240225871, ss3650465189, ss3698853687, ss3818992031 NC_000016.10:10670714:A:C NC_000016.10:10670714:A:C (self)
ss14257530 NT_010393.14:2076783:A:C NC_000016.10:10670714:A:C (self)
ss3562843, ss43899020, ss106461664, ss136592490 NT_010393.16:10704571:A:C NC_000016.10:10670714:A:C (self)
ss3240225872 NC_000016.10:10670714:A:T NC_000016.10:10670714:A:T (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 rs2541505

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.post246+3cda961