Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs10492106

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr12:8093806 (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
T>A / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.045952 (12163/264690, TOPMED)
A=0.046383 (6490/139922, GnomAD)
A=0.05301 (1185/22356, ALFA) (+ 13 more)
A=0.0274 (137/5008, 1000G)
A=0.0391 (175/4480, Estonian)
A=0.0618 (238/3854, ALSPAC)
A=0.0566 (210/3708, TWINSUK)
A=0.082 (82/998, GoNL)
A=0.048 (47/980, HapMap)
A=0.065 (39/600, NorthernSweden)
A=0.028 (6/216, Qatari)
A=0.10 (4/40, GENOME_DK)
T=0.50 (12/24, SGDP_PRJ)
A=0.50 (12/24, SGDP_PRJ)
T=0.5 (2/4, Siberian)
A=0.5 (2/4, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NECAP1 : 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 12 NC_000012.12:g.8093806T>A
GRCh38.p13 chr 12 NC_000012.12:g.8093806T>G
GRCh37.p13 chr 12 NC_000012.11:g.8246402T>A
GRCh37.p13 chr 12 NC_000012.11:g.8246402T>G
NECAP1 RefSeqGene NG_034155.1:g.16596T>A
NECAP1 RefSeqGene NG_034155.1:g.16596T>G
Gene: NECAP1, NECAP endocytosis associated 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
NECAP1 transcript variant 1 NM_015509.4:c.676+751T>A N/A Intron Variant
NECAP1 transcript variant 2 NR_024260.2: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 22356 T=0.94699 A=0.05301, G=0.00000
European Sub 17628 T=0.93709 A=0.06291, G=0.00000
African Sub 2964 T=0.9963 A=0.0037, G=0.0000
African Others Sub 114 T=1.000 A=0.000, G=0.000
African American Sub 2850 T=0.9961 A=0.0039, G=0.0000
Asian Sub 114 T=1.000 A=0.000, G=0.000
East Asian Sub 88 T=1.00 A=0.00, G=0.00
Other Asian Sub 26 T=1.00 A=0.00, G=0.00
Latin American 1 Sub 150 T=0.933 A=0.067, G=0.000
Latin American 2 Sub 626 T=0.981 A=0.019, G=0.000
South Asian Sub 98 T=0.94 A=0.06, G=0.00
Other Sub 776 T=0.952 A=0.048, G=0.000


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 T=0.954048 A=0.045952
gnomAD - Genomes Global Study-wide 139922 T=0.953617 A=0.046383
gnomAD - Genomes European Sub 75774 T=0.93485 A=0.06515
gnomAD - Genomes African Sub 41938 T=0.98667 A=0.01333
gnomAD - Genomes American Sub 13616 T=0.95740 A=0.04260
gnomAD - Genomes Ashkenazi Jewish Sub 3318 T=0.9030 A=0.0970
gnomAD - Genomes East Asian Sub 3128 T=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2148 T=0.9572 A=0.0428
1000Genomes Global Study-wide 5008 T=0.9726 A=0.0274
1000Genomes African Sub 1322 T=0.9977 A=0.0023
1000Genomes East Asian Sub 1008 T=1.0000 A=0.0000
1000Genomes Europe Sub 1006 T=0.9344 A=0.0656
1000Genomes South Asian Sub 978 T=0.968 A=0.032
1000Genomes American Sub 694 T=0.947 A=0.053
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9609 A=0.0391
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9382 A=0.0618
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9434 A=0.0566
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.918 A=0.082
HapMap Global Study-wide 980 T=0.952 A=0.048
HapMap American Sub 600 T=0.948 A=0.052
HapMap Europe Sub 174 T=0.908 A=0.092
HapMap African Sub 120 T=1.000 A=0.000
HapMap Asian Sub 86 T=1.00 A=0.00
Northern Sweden ACPOP Study-wide 600 T=0.935 A=0.065
Qatari Global Study-wide 216 T=0.972 A=0.028
The Danish reference pan genome Danish Study-wide 40 T=0.90 A=0.10
SGDP_PRJ Global Study-wide 24 T=0.50 A=0.50
Siberian Global Study-wide 4 T=0.5 A=0.5
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 G
GRCh38.p13 chr 12 NC_000012.12:g.8093806= NC_000012.12:g.8093806T>A NC_000012.12:g.8093806T>G
GRCh37.p13 chr 12 NC_000012.11:g.8246402= NC_000012.11:g.8246402T>A NC_000012.11:g.8246402T>G
NECAP1 RefSeqGene NG_034155.1:g.16596= NG_034155.1:g.16596T>A NG_034155.1:g.16596T>G
NECAP1 transcript variant 1 NM_015509.3:c.676+751= NM_015509.3:c.676+751T>A NM_015509.3:c.676+751T>G
NECAP1 transcript variant 1 NM_015509.4:c.676+751= NM_015509.4:c.676+751T>A NM_015509.4:c.676+751T>G
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#.

65 SubSNP, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss14880174 Dec 05, 2003 (119)
2 PERLEGEN ss24698397 Sep 20, 2004 (123)
3 AFFY ss65988847 Nov 29, 2006 (127)
4 PERLEGEN ss69100123 May 16, 2007 (127)
5 AFFY ss76493559 Dec 06, 2007 (129)
6 KRIBB_YJKIM ss105009150 Feb 06, 2009 (130)
7 ILLUMINA ss159900717 Dec 01, 2009 (131)
8 ILLUMINA ss170186068 Jul 04, 2010 (132)
9 1000GENOMES ss235813953 Jul 15, 2010 (132)
10 ILLUMINA ss479287321 May 04, 2012 (137)
11 ILLUMINA ss479290369 May 04, 2012 (137)
12 ILLUMINA ss479668862 Sep 08, 2015 (146)
13 ILLUMINA ss484444144 May 04, 2012 (137)
14 ILLUMINA ss536612364 Sep 08, 2015 (146)
15 SSMP ss658506937 Apr 25, 2013 (138)
16 ILLUMINA ss778342336 Sep 08, 2015 (146)
17 ILLUMINA ss782668578 Sep 08, 2015 (146)
18 ILLUMINA ss783637327 Sep 08, 2015 (146)
19 ILLUMINA ss831919210 Sep 08, 2015 (146)
20 ILLUMINA ss833796947 Sep 08, 2015 (146)
21 EVA-GONL ss989213690 Aug 21, 2014 (142)
22 JMKIDD_LAB ss1078230330 Aug 21, 2014 (142)
23 1000GENOMES ss1388061956 Apr 01, 2015 (144)
24 DDI ss1426835255 Apr 01, 2015 (144)
25 EVA_GENOME_DK ss1576099683 Apr 01, 2015 (144)
26 EVA_DECODE ss1598885037 Apr 01, 2015 (144)
27 EVA_UK10K_ALSPAC ss1627973235 Apr 01, 2015 (144)
28 EVA_UK10K_TWINSUK ss1670967268 Apr 01, 2015 (144)
29 EVA_SVP ss1713305252 Apr 01, 2015 (144)
30 ILLUMINA ss1752083430 Sep 08, 2015 (146)
31 WEILL_CORNELL_DGM ss1932576311 Feb 12, 2016 (147)
32 JJLAB ss2027034469 Sep 14, 2016 (149)
33 USC_VALOUEV ss2155355940 Dec 20, 2016 (150)
34 HUMAN_LONGEVITY ss2187633878 Dec 20, 2016 (150)
35 TOPMED ss2351242535 Dec 20, 2016 (150)
36 ILLUMINA ss2632922304 Nov 08, 2017 (151)
37 GNOMAD ss2907086780 Nov 08, 2017 (151)
38 SWEGEN ss3009163686 Nov 08, 2017 (151)
39 BIOINF_KMB_FNS_UNIBA ss3027321373 Nov 08, 2017 (151)
40 TOPMED ss3162383210 Nov 08, 2017 (151)
41 CSHL ss3349910243 Nov 08, 2017 (151)
42 ILLUMINA ss3626811142 Oct 12, 2018 (152)
43 ILLUMINA ss3630934114 Oct 12, 2018 (152)
44 ILLUMINA ss3633009447 Oct 12, 2018 (152)
45 ILLUMINA ss3633709919 Oct 12, 2018 (152)
46 ILLUMINA ss3634489819 Oct 12, 2018 (152)
47 ILLUMINA ss3635400973 Oct 12, 2018 (152)
48 ILLUMINA ss3636173828 Oct 12, 2018 (152)
49 ILLUMINA ss3637151921 Oct 12, 2018 (152)
50 ILLUMINA ss3637945867 Oct 12, 2018 (152)
51 ILLUMINA ss3640197153 Oct 12, 2018 (152)
52 EGCUT_WGS ss3676493370 Jul 13, 2019 (153)
53 EVA_DECODE ss3693069231 Jul 13, 2019 (153)
54 ACPOP ss3738749626 Jul 13, 2019 (153)
55 ILLUMINA ss3744790536 Jul 13, 2019 (153)
56 EVA ss3750113323 Jul 13, 2019 (153)
57 ILLUMINA ss3772290109 Jul 13, 2019 (153)
58 PACBIO ss3787134346 Jul 13, 2019 (153)
59 PACBIO ss3792249465 Jul 13, 2019 (153)
60 PACBIO ss3797132289 Jul 13, 2019 (153)
61 KHV_HUMAN_GENOMES ss3815428649 Jul 13, 2019 (153)
62 EVA ss3832962330 Apr 26, 2020 (154)
63 SGDP_PRJ ss3877638293 Apr 26, 2020 (154)
64 EVA ss4017572943 Apr 26, 2021 (155)
65 TOPMED ss4907944764 Apr 26, 2021 (155)
66 1000Genomes NC_000012.11 - 8246402 Oct 12, 2018 (152)
67 The Avon Longitudinal Study of Parents and Children NC_000012.11 - 8246402 Oct 12, 2018 (152)
68 Genetic variation in the Estonian population NC_000012.11 - 8246402 Oct 12, 2018 (152)
69 The Danish reference pan genome NC_000012.11 - 8246402 Apr 26, 2020 (154)
70 gnomAD - Genomes NC_000012.12 - 8093806 Apr 26, 2021 (155)
71 Genome of the Netherlands Release 5 NC_000012.11 - 8246402 Apr 26, 2020 (154)
72 HapMap NC_000012.12 - 8093806 Apr 26, 2020 (154)
73 Northern Sweden NC_000012.11 - 8246402 Jul 13, 2019 (153)
74 Qatari NC_000012.11 - 8246402 Apr 26, 2020 (154)
75 SGDP_PRJ NC_000012.11 - 8246402 Apr 26, 2020 (154)
76 Siberian NC_000012.11 - 8246402 Apr 26, 2020 (154)
77 TopMed NC_000012.12 - 8093806 Apr 26, 2021 (155)
78 UK 10K study - Twins NC_000012.11 - 8246402 Oct 12, 2018 (152)
79 ALFA NC_000012.12 - 8093806 Apr 26, 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).

Associated ID History Updated (Build)
rs17728796 Oct 08, 2004 (123)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss76493559, ss479287321, ss1598885037, ss1713305252 NC_000012.10:8137668:T:A NC_000012.12:8093805:T:A (self)
56528930, 31392970, 22231618, 2833699, 14003592, 12034491, 14618241, 29655273, 7872294, 31392970, ss235813953, ss479290369, ss479668862, ss484444144, ss536612364, ss658506937, ss778342336, ss782668578, ss783637327, ss831919210, ss833796947, ss989213690, ss1078230330, ss1388061956, ss1426835255, ss1576099683, ss1627973235, ss1670967268, ss1752083430, ss1932576311, ss2027034469, ss2155355940, ss2351242535, ss2632922304, ss2907086780, ss3009163686, ss3349910243, ss3626811142, ss3630934114, ss3633009447, ss3633709919, ss3634489819, ss3635400973, ss3636173828, ss3637151921, ss3637945867, ss3640197153, ss3676493370, ss3738749626, ss3744790536, ss3750113323, ss3772290109, ss3787134346, ss3792249465, ss3797132289, ss3832962330, ss3877638293, ss4017572943 NC_000012.11:8246401:T:A NC_000012.12:8093805:T:A (self)
398634784, 751079, 77378701, 123490421, 8147118751, ss2187633878, ss3027321373, ss3162383210, ss3693069231, ss3815428649, ss4907944764 NC_000012.12:8093805:T:A NC_000012.12:8093805:T:A (self)
ss14880174, ss24698397, ss65988847, ss69100123, ss105009150, ss159900717, ss170186068 NT_009714.17:1006525:T:A NC_000012.12:8093805:T:A (self)
8147118751 NC_000012.12:8093805:T:G NC_000012.12:8093805:T:G
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 rs10492106

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