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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 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.

rs9414742

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr10:60739769 (GRCh38.p13) 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>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.334769 (88610/264690, TOPMED)
T=0.331541 (46372/139868, GnomAD)
T=0.31216 (5690/18228, ALFA) (+ 15 more)
T=0.30173 (5057/16760, 8.3KJPN)
T=0.3427 (1716/5008, 1000G)
T=0.3321 (1488/4480, Estonian)
T=0.3041 (1172/3854, ALSPAC)
T=0.3147 (1167/3708, TWINSUK)
T=0.3747 (1098/2930, KOREAN)
T=0.3755 (688/1832, Korea1K)
T=0.328 (327/998, GoNL)
T=0.328 (197/600, NorthernSweden)
T=0.327 (106/324, HapMap)
C=0.416 (129/310, SGDP_PRJ)
T=0.356 (77/216, Qatari)
C=0.454 (98/216, Vietnamese)
T=0.42 (17/40, GENOME_DK)
C=0.27 (6/22, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ANK3-DT : 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.p13 chr 10 NC_000010.11:g.60739769C>A
GRCh38.p13 chr 10 NC_000010.11:g.60739769C>T
GRCh37.p13 chr 10 NC_000010.10:g.62499527C>A
GRCh37.p13 chr 10 NC_000010.10:g.62499527C>T
Gene: ANK3-DT, uncharacterized ANK3-DT (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ANK3-DT transcript variant X1 XR_001747686.1:n. N/A Intron Variant
ANK3-DT transcript variant X2 XR_001747687.1:n. 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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 18228 C=0.68784 A=0.00000, T=0.31216
European Sub 13952 C=0.69818 A=0.00000, T=0.30182
African Sub 2618 C=0.6520 A=0.0000, T=0.3480
African Others Sub 94 C=0.71 A=0.00, T=0.29
African American Sub 2524 C=0.6498 A=0.0000, T=0.3502
Asian Sub 112 C=0.482 A=0.000, T=0.518
East Asian Sub 86 C=0.51 A=0.00, T=0.49
Other Asian Sub 26 C=0.38 A=0.00, T=0.62
Latin American 1 Sub 146 C=0.712 A=0.000, T=0.288
Latin American 2 Sub 610 C=0.662 A=0.000, T=0.338
South Asian Sub 98 C=0.80 A=0.00, T=0.20
Other Sub 692 C=0.650 A=0.000, T=0.350


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 C=0.665231 T=0.334769
gnomAD - Genomes Global Study-wide 139868 C=0.668459 T=0.331541
gnomAD - Genomes European Sub 75772 C=0.68965 T=0.31035
gnomAD - Genomes African Sub 41868 C=0.61949 T=0.38051
gnomAD - Genomes American Sub 13640 C=0.70330 T=0.29670
gnomAD - Genomes Ashkenazi Jewish Sub 3318 C=0.7815 T=0.2185
gnomAD - Genomes East Asian Sub 3118 C=0.5327 T=0.4673
gnomAD - Genomes Other Sub 2152 C=0.6766 T=0.3234
8.3KJPN JAPANESE Study-wide 16760 C=0.69827 T=0.30173
1000Genomes Global Study-wide 5008 C=0.6573 T=0.3427
1000Genomes African Sub 1322 C=0.5991 T=0.4009
1000Genomes East Asian Sub 1008 C=0.5327 T=0.4673
1000Genomes Europe Sub 1006 C=0.7087 T=0.2913
1000Genomes South Asian Sub 978 C=0.797 T=0.203
1000Genomes American Sub 694 C=0.679 T=0.321
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.6679 T=0.3321
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.6959 T=0.3041
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.6853 T=0.3147
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.6253 T=0.3747
Korean Genome Project KOREAN Study-wide 1832 C=0.6245 T=0.3755
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.672 T=0.328
Northern Sweden ACPOP Study-wide 600 C=0.672 T=0.328
HapMap Global Study-wide 324 C=0.673 T=0.327
HapMap African Sub 120 C=0.592 T=0.408
HapMap American Sub 118 C=0.712 T=0.288
HapMap Asian Sub 86 C=0.73 T=0.27
SGDP_PRJ Global Study-wide 310 C=0.416 T=0.584
Qatari Global Study-wide 216 C=0.644 T=0.356
A Vietnamese Genetic Variation Database Global Study-wide 216 C=0.454 T=0.546
The Danish reference pan genome Danish Study-wide 40 C=0.57 T=0.42
Siberian Global Study-wide 22 C=0.27 T=0.73
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= A T
GRCh38.p13 chr 10 NC_000010.11:g.60739769= NC_000010.11:g.60739769C>A NC_000010.11:g.60739769C>T
GRCh37.p13 chr 10 NC_000010.10:g.62499527= NC_000010.10:g.62499527C>A NC_000010.10:g.62499527C>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#.

56 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss12953972 Dec 05, 2003 (119)
2 CSHL-HAPMAP ss19155954 Feb 27, 2004 (120)
3 PERLEGEN ss24059104 Sep 20, 2004 (123)
4 ABI ss38565373 Mar 13, 2006 (126)
5 HGSV ss78083792 Dec 06, 2007 (129)
6 1000GENOMES ss109490775 Jan 24, 2009 (130)
7 1000GENOMES ss113347315 Jan 25, 2009 (130)
8 ILLUMINA-UK ss119190042 Feb 15, 2009 (130)
9 GMI ss155112004 Dec 01, 2009 (131)
10 ENSEMBL ss161351845 Dec 01, 2009 (131)
11 COMPLETE_GENOMICS ss170175160 Jul 04, 2010 (132)
12 COMPLETE_GENOMICS ss174574902 Jul 04, 2010 (132)
13 BCM-HGSC-SUB ss207272878 Jul 04, 2010 (132)
14 1000GENOMES ss224758217 Jul 14, 2010 (132)
15 1000GENOMES ss235199244 Jul 15, 2010 (132)
16 1000GENOMES ss241900492 Jul 15, 2010 (132)
17 GMI ss280640372 May 04, 2012 (137)
18 PJP ss290850622 May 09, 2011 (134)
19 TISHKOFF ss561992878 Apr 25, 2013 (138)
20 SSMP ss656817582 Apr 25, 2013 (138)
21 EVA-GONL ss987549617 Aug 21, 2014 (142)
22 JMKIDD_LAB ss1077032126 Aug 21, 2014 (142)
23 1000GENOMES ss1337666916 Aug 21, 2014 (142)
24 DDI ss1426339506 Apr 01, 2015 (144)
25 EVA_GENOME_DK ss1575154095 Apr 01, 2015 (144)
26 EVA_DECODE ss1597216073 Apr 01, 2015 (144)
27 EVA_UK10K_ALSPAC ss1624686409 Apr 01, 2015 (144)
28 EVA_UK10K_TWINSUK ss1667680442 Apr 01, 2015 (144)
29 HAMMER_LAB ss1806415889 Sep 08, 2015 (146)
30 WEILL_CORNELL_DGM ss1930913537 Feb 12, 2016 (147)
31 GENOMED ss1967142909 Jul 19, 2016 (147)
32 JJLAB ss2026180013 Sep 14, 2016 (149)
33 USC_VALOUEV ss2154453162 Dec 20, 2016 (150)
34 HUMAN_LONGEVITY ss2175215839 Dec 20, 2016 (150)
35 TOPMED ss2338248198 Dec 20, 2016 (150)
36 GRF ss2698697277 Nov 08, 2017 (151)
37 GNOMAD ss2889428050 Nov 08, 2017 (151)
38 SWEGEN ss3006572560 Nov 08, 2017 (151)
39 BIOINF_KMB_FNS_UNIBA ss3026881147 Nov 08, 2017 (151)
40 TOPMED ss3121331098 Nov 08, 2017 (151)
41 CSHL ss3349150221 Nov 08, 2017 (151)
42 EGCUT_WGS ss3673985029 Jul 13, 2019 (153)
43 ACPOP ss3737372896 Jul 13, 2019 (153)
44 EVA ss3748171581 Jul 13, 2019 (153)
45 PACBIO ss3786688955 Jul 13, 2019 (153)
46 PACBIO ss3791867462 Jul 13, 2019 (153)
47 PACBIO ss3796749480 Jul 13, 2019 (153)
48 KHV_HUMAN_GENOMES ss3813547251 Jul 13, 2019 (153)
49 EVA ss3832155482 Apr 26, 2020 (154)
50 EVA ss3839617213 Apr 26, 2020 (154)
51 EVA ss3845089451 Apr 26, 2020 (154)
52 SGDP_PRJ ss3874329267 Apr 26, 2020 (154)
53 KRGDB ss3922399231 Apr 26, 2020 (154)
54 KOGIC ss3967991994 Apr 26, 2020 (154)
55 TOPMED ss4854398031 Apr 27, 2021 (155)
56 TOMMO_GENOMICS ss5197890495 Apr 27, 2021 (155)
57 1000Genomes NC_000010.10 - 62499527 Oct 12, 2018 (152)
58 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 62499527 Oct 12, 2018 (152)
59 Genetic variation in the Estonian population NC_000010.10 - 62499527 Oct 12, 2018 (152)
60 The Danish reference pan genome NC_000010.10 - 62499527 Apr 26, 2020 (154)
61 gnomAD - Genomes NC_000010.11 - 60739769 Apr 27, 2021 (155)
62 Genome of the Netherlands Release 5 NC_000010.10 - 62499527 Apr 26, 2020 (154)
63 HapMap NC_000010.11 - 60739769 Apr 26, 2020 (154)
64 KOREAN population from KRGDB NC_000010.10 - 62499527 Apr 26, 2020 (154)
65 Korean Genome Project NC_000010.11 - 60739769 Apr 26, 2020 (154)
66 Northern Sweden NC_000010.10 - 62499527 Jul 13, 2019 (153)
67 Qatari NC_000010.10 - 62499527 Apr 26, 2020 (154)
68 SGDP_PRJ NC_000010.10 - 62499527 Apr 26, 2020 (154)
69 Siberian NC_000010.10 - 62499527 Apr 26, 2020 (154)
70 8.3KJPN NC_000010.10 - 62499527 Apr 27, 2021 (155)
71 TopMed NC_000010.11 - 60739769 Apr 27, 2021 (155)
72 UK 10K study - Twins NC_000010.10 - 62499527 Oct 12, 2018 (152)
73 A Vietnamese Genetic Variation Database NC_000010.10 - 62499527 Jul 13, 2019 (153)
74 ALFA NC_000010.11 - 60739769 Apr 27, 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
6613522152 NC_000010.11:60739768:C:A NC_000010.11:60739768:C:A
ss78083792 NC_000010.8:62169532:C:T NC_000010.11:60739768:C:T (self)
ss109490775, ss113347315, ss119190042, ss170175160, ss174574902, ss207272878, ss280640372, ss290850622, ss1597216073 NC_000010.9:62169532:C:T NC_000010.11:60739768:C:T (self)
50063242, 27785651, 19723277, 2181547, 12392032, 29576625, 10657761, 12955467, 26346247, 6969516, 55859802, 27785651, 6171091, ss224758217, ss235199244, ss241900492, ss561992878, ss656817582, ss987549617, ss1077032126, ss1337666916, ss1426339506, ss1575154095, ss1624686409, ss1667680442, ss1806415889, ss1930913537, ss1967142909, ss2026180013, ss2154453162, ss2338248198, ss2698697277, ss2889428050, ss3006572560, ss3349150221, ss3673985029, ss3737372896, ss3748171581, ss3786688955, ss3791867462, ss3796749480, ss3832155482, ss3839617213, ss3874329267, ss3922399231, ss5197890495 NC_000010.10:62499526:C:T NC_000010.11:60739768:C:T (self)
353865639, 415644, 24369995, 43946991, 69943686, 6613522152, ss2175215839, ss3026881147, ss3121331098, ss3813547251, ss3845089451, ss3967991994, ss4854398031 NC_000010.11:60739768:C:T NC_000010.11:60739768:C:T (self)
ss12953972 NT_008583.15:11050674:C:T NC_000010.11:60739768:C:T (self)
ss19155954 NT_008583.16:11050681:C:T NC_000010.11:60739768:C:T (self)
ss24059104, ss38565373, ss155112004, ss161351845 NT_030059.13:13303990:C:T NC_000010.11:60739768: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 rs9414742

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.post596+ae089ad