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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.

rs10492116

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr12:21474591 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.03311 (4157/125568, TOPMED)
T=0.0268 (829/30922, GnomAD)
T=0.025 (124/5008, 1000G) (+ 3 more)
T=0.026 (117/4480, Estonian)
T=0.046 (177/3854, ALSPAC)
T=0.053 (198/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RECQL : 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 12 NC_000012.12:g.21474591C>T
GRCh37.p13 chr 12 NC_000012.11:g.21627525C>T
Gene: RECQL, RecQ like helicase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
RECQL transcript variant 1 NM_002907.3:c. N/A Intron Variant
RECQL transcript variant 2 NM_032941.2:c. N/A Intron Variant
RECQL transcript variant X2 XM_005253461.3:c. N/A Intron Variant
RECQL transcript variant X4 XM_005253462.5:c. N/A Intron Variant
RECQL transcript variant X3 XM_005253463.4:c. N/A Intron Variant
RECQL transcript variant X1 XM_005253464.4: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").

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Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 C=0.96689 T=0.03311
gnomAD - Genomes Global Study-wide 30922 C=0.9732 T=0.0268
gnomAD - Genomes European Sub 18460 C=0.9621 T=0.0379
gnomAD - Genomes African Sub 8732 C=0.993 T=0.007
gnomAD - Genomes East Asian Sub 1612 C=0.999 T=0.001
gnomAD - Genomes Other Sub 980 C=0.96 T=0.04
gnomAD - Genomes American Sub 836 C=0.98 T=0.02
gnomAD - Genomes Ashkenazi Jewish Sub 302 C=0.95 T=0.05
1000Genomes Global Study-wide 5008 C=0.975 T=0.025
1000Genomes African Sub 1322 C=0.999 T=0.001
1000Genomes East Asian Sub 1008 C=1.000 T=0.000
1000Genomes Europe Sub 1006 C=0.939 T=0.061
1000Genomes South Asian Sub 978 C=0.97 T=0.03
1000Genomes American Sub 694 C=0.95 T=0.05
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.974 T=0.026
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.954 T=0.046
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.947 T=0.053
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 C= T Note
GRCh38.p12 chr 12 NC_000012.12:g.21474591C= NC_000012.12:g.21474591C>T
GRCh37.p13 chr 12 NC_000012.11:g.21627525C= NC_000012.11:g.21627525C>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#.

45 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss14880189 Dec 05, 2003 (119)
2 PERLEGEN ss24380639 Sep 20, 2004 (123)
3 AFFY ss65989173 Nov 30, 2006 (127)
4 ILLUMINA ss66570115 Nov 30, 2006 (127)
5 ILLUMINA ss66887341 Nov 30, 2006 (127)
6 ILLUMINA ss66986752 Nov 30, 2006 (127)
7 ILLUMINA ss70368875 May 17, 2007 (127)
8 ILLUMINA ss70483184 May 25, 2008 (130)
9 ILLUMINA ss71007144 May 17, 2007 (127)
10 ILLUMINA ss74952071 Dec 07, 2007 (129)
11 KRIBB_YJKIM ss84951164 Dec 15, 2007 (130)
12 CNG ss98335728 Feb 05, 2009 (130)
13 ILLUMINA ss121324172 Dec 01, 2009 (131)
14 ILLUMINA ss152748799 Dec 01, 2009 (131)
15 ILLUMINA ss159128083 Dec 01, 2009 (131)
16 ILLUMINA ss169438161 Jul 04, 2010 (132)
17 ILLUMINA ss170186130 Jul 04, 2010 (132)
18 1000GENOMES ss235855442 Jul 15, 2010 (132)
19 ILLUMINA ss536612370 Sep 08, 2015 (146)
20 SSMP ss658577524 Apr 25, 2013 (138)
21 ILLUMINA ss825338486 Jul 19, 2016 (147)
22 EVA-GONL ss989319585 Aug 21, 2014 (142)
23 JMKIDD_LAB ss1078307363 Aug 21, 2014 (142)
24 1000GENOMES ss1344214058 Aug 21, 2014 (142)
25 HAMMER_LAB ss1397628354 Sep 08, 2015 (146)
26 EVA_DECODE ss1598992284 Apr 01, 2015 (144)
27 EVA_UK10K_ALSPAC ss1628171419 Apr 01, 2015 (144)
28 EVA_UK10K_TWINSUK ss1671165452 Apr 01, 2015 (144)
29 EVA_SVP ss1713312962 Apr 01, 2015 (144)
30 WEILL_CORNELL_DGM ss1932684283 Feb 12, 2016 (147)
31 JJLAB ss2027089573 Sep 14, 2016 (149)
32 USC_VALOUEV ss2155415331 Dec 20, 2016 (150)
33 HUMAN_LONGEVITY ss2188391803 Dec 20, 2016 (150)
34 TOPMED ss2352049860 Dec 20, 2016 (150)
35 GNOMAD ss2908199690 Nov 08, 2017 (151)
36 AFFY ss2985612583 Nov 08, 2017 (151)
37 SWEGEN ss3009334461 Nov 08, 2017 (151)
38 BIOINF_KMB_FNS_UNIBA ss3027351187 Nov 08, 2017 (151)
39 TOPMED ss3164924982 Nov 08, 2017 (151)
40 CSHL ss3349962111 Nov 08, 2017 (151)
41 ILLUMINA ss3626834093 Oct 12, 2018 (152)
42 ILLUMINA ss3637951895 Oct 12, 2018 (152)
43 ILLUMINA ss3638989744 Oct 12, 2018 (152)
44 ILLUMINA ss3639496752 Oct 12, 2018 (152)
45 ILLUMINA ss3642946437 Oct 12, 2018 (152)
46 1000Genomes NC_000012.11 - 21627525 Oct 12, 2018 (152)
47 The Avon Longitudinal Study of Parents and Children NC_000012.11 - 21627525 Oct 12, 2018 (152)
48 Genetic variation in the Estonian population NC_000012.11 - 21627525 Oct 12, 2018 (152)
49 gnomAD - Genomes NC_000012.11 - 21627525 Oct 12, 2018 (152)
50 TopMed NC_000012.12 - 21474591 Oct 12, 2018 (152)
51 UK 10K study - Twins NC_000012.11 - 21627525 Oct 12, 2018 (152)
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)
rs17683293 Oct 08, 2004 (123)
rs58923942 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss3638989744, ss3639496752 NC_000012.9:21518791:C= NC_000012.12:21474590:C=
ss825338486, ss1397628354, ss1598992284, ss1713312962, ss3642946437 NC_000012.10:21518791:C= NC_000012.12:21474590:C= (self)
56933074, 31612576, 22388161, 41901213, 31612576, ss235855442, ss536612370, ss658577524, ss989319585, ss1078307363, ss1344214058, ss1628171419, ss1671165452, ss1932684283, ss2027089573, ss2155415331, ss2352049860, ss2908199690, ss2985612583, ss3009334461, ss3349962111, ss3626834093, ss3637951895 NC_000012.11:21627524:C= NC_000012.12:21474590:C= (self)
79468789, ss2188391803, ss3027351187, ss3164924982 NC_000012.12:21474590:C= NC_000012.12:21474590:C= (self)
ss14880189, ss24380639, ss65989173, ss66570115, ss66887341, ss66986752, ss70368875, ss70483184, ss71007144, ss74952071, ss84951164, ss98335728, ss121324172, ss152748799, ss159128083, ss169438161, ss170186130 NT_009714.17:14387648:C= NC_000012.12:21474590:C= (self)
ss3638989744, ss3639496752 NC_000012.9:21518791:C>T NC_000012.12:21474590:C>T
ss825338486, ss1397628354, ss1598992284, ss1713312962, ss3642946437 NC_000012.10:21518791:C>T NC_000012.12:21474590:C>T (self)
56933074, 31612576, 22388161, 41901213, 31612576, ss235855442, ss536612370, ss658577524, ss989319585, ss1078307363, ss1344214058, ss1628171419, ss1671165452, ss1932684283, ss2027089573, ss2155415331, ss2352049860, ss2908199690, ss2985612583, ss3009334461, ss3349962111, ss3626834093, ss3637951895 NC_000012.11:21627524:C>T NC_000012.12:21474590:C>T (self)
79468789, ss2188391803, ss3027351187, ss3164924982 NC_000012.12:21474590:C>T NC_000012.12:21474590:C>T (self)
ss14880189, ss24380639, ss65989173, ss66570115, ss66887341, ss66986752, ss70368875, ss70483184, ss71007144, ss74952071, ss84951164, ss98335728, ss121324172, ss152748799, ss159128083, ss169438161, ss170186130 NT_009714.17:14387648:C>T NC_000012.12:21474590:C>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 rs10492116

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.post58+e54ea20