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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.

rs139143465

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:6472031 (GRCh38.p14) 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=0.000967 (256/264690, TOPMED)
T=0.003759 (527/140206, GnomAD)
T=0.00028 (8/28258, 14KJPN) (+ 11 more)
T=0.00307 (58/18890, ALFA)
T=0.00024 (4/16758, 8.3KJPN)
T=0.0017 (11/6404, 1000G_30x)
T=0.0022 (11/5008, 1000G)
T=0.0096 (43/4480, Estonian)
T=0.0018 (7/3854, ALSPAC)
T=0.0032 (12/3708, TWINSUK)
T=0.0010 (3/2922, KOREAN)
T=0.0005 (1/1832, Korea1K)
T=0.001 (1/998, GoNL)
T=0.003 (2/600, NorthernSweden)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TRIM3 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome

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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 18890 C=0.99693 T=0.00307
European Sub 14286 C=0.99615 T=0.00385
African Sub 2946 C=0.9993 T=0.0007
African Others Sub 114 C=1.000 T=0.000
African American Sub 2832 C=0.9993 T=0.0007
Asian Sub 112 C=1.000 T=0.000
East Asian Sub 86 C=1.00 T=0.00
Other Asian Sub 26 C=1.00 T=0.00
Latin American 1 Sub 146 C=1.000 T=0.000
Latin American 2 Sub 610 C=0.998 T=0.002
South Asian Sub 98 C=1.00 T=0.00
Other Sub 692 C=1.000 T=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 C=0.999033 T=0.000967
gnomAD - Genomes Global Study-wide 140206 C=0.996241 T=0.003759
gnomAD - Genomes European Sub 75918 C=0.99348 T=0.00652
gnomAD - Genomes African Sub 42032 C=0.99967 T=0.00033
gnomAD - Genomes American Sub 13646 C=0.99949 T=0.00051
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.9982 T=0.0018
gnomAD - Genomes East Asian Sub 3134 C=0.9994 T=0.0006
gnomAD - Genomes Other Sub 2154 C=0.9986 T=0.0014
14KJPN JAPANESE Study-wide 28258 C=0.99972 T=0.00028
Allele Frequency Aggregator Total Global 18890 C=0.99693 T=0.00307
Allele Frequency Aggregator European Sub 14286 C=0.99615 T=0.00385
Allele Frequency Aggregator African Sub 2946 C=0.9993 T=0.0007
Allele Frequency Aggregator Other Sub 692 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.998 T=0.002
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
8.3KJPN JAPANESE Study-wide 16758 C=0.99976 T=0.00024
1000Genomes_30x Global Study-wide 6404 C=0.9983 T=0.0017
1000Genomes_30x African Sub 1786 C=0.9994 T=0.0006
1000Genomes_30x Europe Sub 1266 C=0.9921 T=0.0079
1000Genomes_30x South Asian Sub 1202 C=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 C=1.0000 T=0.0000
1000Genomes_30x American Sub 980 C=1.000 T=0.000
1000Genomes Global Study-wide 5008 C=0.9978 T=0.0022
1000Genomes African Sub 1322 C=0.9992 T=0.0008
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=0.9911 T=0.0089
1000Genomes South Asian Sub 978 C=0.999 T=0.001
1000Genomes American Sub 694 C=1.000 T=0.000
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9904 T=0.0096
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9982 T=0.0018
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9968 T=0.0032
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.9990 T=0.0010
Korean Genome Project KOREAN Study-wide 1832 C=0.9995 T=0.0005
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.999 T=0.001
Northern Sweden ACPOP Study-wide 600 C=0.997 T=0.003
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.p14 chr 11 NC_000011.10:g.6472031C>T
GRCh37.p13 chr 11 NC_000011.9:g.6493261C>T
Gene: TRIM3, tripartite motif containing 3 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TRIM3 transcript variant 4 NM_001248006.2:c.-38+2071…

NM_001248006.2:c.-38+2071G>A

N/A Intron Variant
TRIM3 transcript variant 5 NM_001248007.2:c.-222+176…

NM_001248007.2:c.-222+1760G>A

N/A Intron Variant
TRIM3 transcript variant 1 NM_006458.4:c.-38+1053G>A N/A Intron Variant
TRIM3 transcript variant 2 NM_033278.4:c.-38+1760G>A N/A Intron Variant
TRIM3 transcript variant X4 XM_017017098.3:c.-38+1734…

XM_017017098.3:c.-38+1734G>A

N/A Intron Variant
TRIM3 transcript variant X3 XM_024448328.2:c.-38+1053…

XM_024448328.2:c.-38+1053G>A

N/A Intron Variant
TRIM3 transcript variant X1 XM_047426257.1:c.212+1053…

XM_047426257.1:c.212+1053G>A

N/A Intron Variant
TRIM3 transcript variant X2 XM_047426258.1:c.47+1580G…

XM_047426258.1:c.47+1580G>A

N/A Intron Variant
TRIM3 transcript variant X6 XM_047426261.1:c.-125+176…

XM_047426261.1:c.-125+1760G>A

N/A Intron Variant
TRIM3 transcript variant X7 XM_047426262.1:c.47+1580G…

XM_047426262.1:c.47+1580G>A

N/A Intron Variant
TRIM3 transcript variant X5 XM_047426259.1:c. N/A Genic Upstream Transcript 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

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
GRCh38.p14 chr 11 NC_000011.10:g.6472031= NC_000011.10:g.6472031C>T
GRCh37.p13 chr 11 NC_000011.9:g.6493261= NC_000011.9:g.6493261C>T
TRIM3 transcript variant 4 NM_001248006.1:c.-38+2071= NM_001248006.1:c.-38+2071G>A
TRIM3 transcript variant 4 NM_001248006.2:c.-38+2071= NM_001248006.2:c.-38+2071G>A
TRIM3 transcript variant 5 NM_001248007.1:c.-222+1760= NM_001248007.1:c.-222+1760G>A
TRIM3 transcript variant 5 NM_001248007.2:c.-222+1760= NM_001248007.2:c.-222+1760G>A
TRIM3 transcript variant 1 NM_006458.3:c.-38+1053= NM_006458.3:c.-38+1053G>A
TRIM3 transcript variant 1 NM_006458.4:c.-38+1053= NM_006458.4:c.-38+1053G>A
TRIM3 transcript variant 2 NM_033278.3:c.-38+1760= NM_033278.3:c.-38+1760G>A
TRIM3 transcript variant 2 NM_033278.4:c.-38+1760= NM_033278.4:c.-38+1760G>A
TRIM3 transcript variant X1 XM_005252751.1:c.-38+1053= XM_005252751.1:c.-38+1053G>A
TRIM3 transcript variant X2 XM_005252752.1:c.-390+1760= XM_005252752.1:c.-390+1760G>A
TRIM3 transcript variant X4 XM_017017098.3:c.-38+1734= XM_017017098.3:c.-38+1734G>A
TRIM3 transcript variant X3 XM_024448328.2:c.-38+1053= XM_024448328.2:c.-38+1053G>A
TRIM3 transcript variant X1 XM_047426257.1:c.212+1053= XM_047426257.1:c.212+1053G>A
TRIM3 transcript variant X2 XM_047426258.1:c.47+1580= XM_047426258.1:c.47+1580G>A
TRIM3 transcript variant X6 XM_047426261.1:c.-125+1760= XM_047426261.1:c.-125+1760G>A
TRIM3 transcript variant X7 XM_047426262.1:c.47+1580= XM_047426262.1:c.47+1580G>A
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#.

24 SubSNP, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss336525877 May 09, 2011 (134)
2 EVA-GONL ss988171249 Aug 21, 2014 (142)
3 1000GENOMES ss1339980783 Aug 21, 2014 (142)
4 EVA_DECODE ss1597847232 Apr 01, 2015 (144)
5 EVA_UK10K_ALSPAC ss1625916918 Apr 01, 2015 (144)
6 EVA_UK10K_TWINSUK ss1668910951 Apr 01, 2015 (144)
7 HUMAN_LONGEVITY ss2179908893 Dec 20, 2016 (150)
8 GNOMAD ss2895951398 Nov 08, 2017 (151)
9 SWEGEN ss3007541002 Nov 08, 2017 (151)
10 EGCUT_WGS ss3674937084 Jul 13, 2019 (153)
11 EVA_DECODE ss3691147342 Jul 13, 2019 (153)
12 ACPOP ss3737889215 Jul 13, 2019 (153)
13 KRGDB ss3923799470 Apr 26, 2020 (154)
14 KOGIC ss3969139634 Apr 26, 2020 (154)
15 TOPMED ss4874026257 Apr 26, 2021 (155)
16 TOMMO_GENOMICS ss5200534213 Apr 26, 2021 (155)
17 1000G_HIGH_COVERAGE ss5286286428 Oct 16, 2022 (156)
18 EVA ss5397525618 Oct 16, 2022 (156)
19 HUGCELL_USP ss5481601462 Oct 16, 2022 (156)
20 1000G_HIGH_COVERAGE ss5581348603 Oct 16, 2022 (156)
21 TOMMO_GENOMICS ss5747246105 Oct 16, 2022 (156)
22 EVA ss5836215644 Oct 16, 2022 (156)
23 EVA ss5918692726 Oct 16, 2022 (156)
24 EVA ss5941872182 Oct 16, 2022 (156)
25 1000Genomes NC_000011.9 - 6493261 Oct 12, 2018 (152)
26 1000Genomes_30x NC_000011.10 - 6472031 Oct 16, 2022 (156)
27 The Avon Longitudinal Study of Parents and Children NC_000011.9 - 6493261 Oct 12, 2018 (152)
28 Genetic variation in the Estonian population NC_000011.9 - 6493261 Oct 12, 2018 (152)
29 gnomAD - Genomes NC_000011.10 - 6472031 Apr 26, 2021 (155)
30 Genome of the Netherlands Release 5 NC_000011.9 - 6493261 Apr 26, 2020 (154)
31 KOREAN population from KRGDB NC_000011.9 - 6493261 Apr 26, 2020 (154)
32 Korean Genome Project NC_000011.10 - 6472031 Apr 26, 2020 (154)
33 Northern Sweden NC_000011.9 - 6493261 Jul 13, 2019 (153)
34 8.3KJPN NC_000011.9 - 6493261 Apr 26, 2021 (155)
35 14KJPN NC_000011.10 - 6472031 Oct 16, 2022 (156)
36 TopMed NC_000011.10 - 6472031 Apr 26, 2021 (155)
37 UK 10K study - Twins NC_000011.9 - 6493261 Oct 12, 2018 (152)
38 ALFA NC_000011.10 - 6472031 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss1597847232 NC_000011.8:6449836:C:T NC_000011.10:6472030:C:T (self)
52458767, 29136433, 20675332, 12991079, 30976864, 11174080, 58503520, 29136433, ss336525877, ss988171249, ss1339980783, ss1625916918, ss1668910951, ss2895951398, ss3007541002, ss3674937084, ss3737889215, ss3923799470, ss5200534213, ss5397525618, ss5836215644, ss5941872182 NC_000011.9:6493260:C:T NC_000011.10:6472030:C:T (self)
68874538, 370391549, 25517635, 81083209, 89571913, 3718110971, ss2179908893, ss3691147342, ss3969139634, ss4874026257, ss5286286428, ss5481601462, ss5581348603, ss5747246105, ss5918692726 NC_000011.10:6472030:C:T NC_000011.10:6472030: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 rs139143465

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.post761+d5e8e07