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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.

rs6858735

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr4:37914606 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.036752 (9728/264690, TOPMED)
T=0.035089 (4920/140216, GnomAD)
T=0.02183 (718/32898, ALFA) (+ 8 more)
T=0.0359 (180/5008, 1000G)
T=0.0002 (1/4480, Estonian)
T=0.001 (1/998, GoNL)
T=0.068 (52/766, HapMap)
T=0.010 (6/626, Chileans)
T=0.028 (6/216, Qatari)
C=0.50 (6/12, SGDP_PRJ)
T=0.50 (6/12, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TBC1D1 : Intron Variant
Publications
1 citation
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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 32898 C=0.97817 T=0.02183
European Sub 24730 C=0.99919 T=0.00081
African Sub 5802 C=0.8871 T=0.1129
African Others Sub 208 C=0.865 T=0.135
African American Sub 5594 C=0.8879 T=0.1121
Asian Sub 128 C=1.000 T=0.000
East Asian Sub 100 C=1.00 T=0.00
Other Asian Sub 28 C=1.00 T=0.00
Latin American 1 Sub 168 C=0.952 T=0.048
Latin American 2 Sub 700 C=0.993 T=0.007
South Asian Sub 114 C=1.000 T=0.000
Other Sub 1256 C=0.9761 T=0.0239


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 264690 C=0.963248 T=0.036752
gnomAD - Genomes Global Study-wide 140216 C=0.964911 T=0.035089
gnomAD - Genomes European Sub 75942 C=0.99934 T=0.00066
gnomAD - Genomes African Sub 42012 C=0.89032 T=0.10968
gnomAD - Genomes American Sub 13656 C=0.98550 T=0.01450
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.9994 T=0.0006
gnomAD - Genomes East Asian Sub 3134 C=0.9997 T=0.0003
gnomAD - Genomes Other Sub 2150 C=0.9716 T=0.0284
1000Genomes Global Study-wide 5008 C=0.9641 T=0.0359
1000Genomes African Sub 1322 C=0.8722 T=0.1278
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=1.0000 T=0.0000
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=0.984 T=0.016
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9998 T=0.0002
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.999 T=0.001
HapMap Global Study-wide 766 C=0.932 T=0.068
HapMap African Sub 296 C=0.851 T=0.149
HapMap American Sub 214 C=0.967 T=0.033
HapMap Europe Sub 168 C=0.994 T=0.006
HapMap Asian Sub 88 C=1.00 T=0.00
Chileans Chilean Study-wide 626 C=0.990 T=0.010
Qatari Global Study-wide 216 C=0.972 T=0.028
SGDP_PRJ Global Study-wide 12 C=0.50 T=0.50
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 4 NC_000004.12:g.37914606C>T
GRCh37.p13 chr 4 NC_000004.11:g.37916227C>T
Gene: TBC1D1, TBC1 domain family member 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TBC1D1 transcript variant 2 NM_001253912.2:c.417+1209…

NM_001253912.2:c.417+12094C>T

N/A Intron Variant
TBC1D1 transcript variant 1 NM_015173.4:c.417+12094C>T N/A Intron Variant
TBC1D1 transcript variant 3 NM_001253913.2:c. N/A Genic Upstream Transcript Variant
TBC1D1 transcript variant 4 NM_001253914.2:c. N/A Genic Upstream Transcript Variant
TBC1D1 transcript variant 5 NM_001253915.2:c. N/A Genic Upstream Transcript Variant
TBC1D1 transcript variant X3 XM_005262646.3:c.417+1209…

XM_005262646.3:c.417+12094C>T

N/A Intron Variant
TBC1D1 transcript variant X4 XM_005262647.3:c.417+1209…

XM_005262647.3:c.417+12094C>T

N/A Intron Variant
TBC1D1 transcript variant X1 XM_011513659.2:c.417+1209…

XM_011513659.2:c.417+12094C>T

N/A Intron Variant
TBC1D1 transcript variant X2 XM_011513660.3:c.417+1209…

XM_011513660.3:c.417+12094C>T

N/A Intron Variant
TBC1D1 transcript variant X5 XM_011513662.3:c.417+1209…

XM_011513662.3:c.417+12094C>T

N/A Intron Variant
TBC1D1 transcript variant X6 XM_011513663.3:c.417+1209…

XM_011513663.3:c.417+12094C>T

N/A Intron Variant
TBC1D1 transcript variant X7 XM_011513664.3:c.417+1209…

XM_011513664.3:c.417+12094C>T

N/A Intron Variant
TBC1D1 transcript variant X10 XM_011513665.3:c.417+1209…

XM_011513665.3:c.417+12094C>T

N/A Intron Variant
TBC1D1 transcript variant X11 XM_011513666.3:c.417+1209…

XM_011513666.3:c.417+12094C>T

N/A Intron Variant
TBC1D1 transcript variant X17 XM_011513668.2:c.417+1209…

XM_011513668.2:c.417+12094C>T

N/A Intron Variant
TBC1D1 transcript variant X8 XM_017007918.2:c.417+1209…

XM_017007918.2:c.417+12094C>T

N/A Intron Variant
TBC1D1 transcript variant X9 XM_017007919.2:c.417+1209…

XM_017007919.2:c.417+12094C>T

N/A Intron Variant
TBC1D1 transcript variant X12 XM_017007920.2:c.417+1209…

XM_017007920.2:c.417+12094C>T

N/A Intron Variant
TBC1D1 transcript variant X15 XM_017007922.1:c.417+1209…

XM_017007922.1:c.417+12094C>T

N/A Intron Variant
TBC1D1 transcript variant X13 XM_005262649.3:c. N/A Genic Upstream Transcript Variant
TBC1D1 transcript variant X18 XM_006714001.3:c. N/A Genic Upstream Transcript Variant
TBC1D1 transcript variant X19 XM_011513670.3:c. N/A Genic Upstream Transcript Variant
TBC1D1 transcript variant X14 XM_017007921.2:c. N/A Genic Upstream Transcript Variant
TBC1D1 transcript variant X16 XR_001741181.1: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
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.p13 chr 4 NC_000004.12:g.37914606= NC_000004.12:g.37914606C>T
GRCh37.p13 chr 4 NC_000004.11:g.37916227= NC_000004.11:g.37916227C>T
TBC1D1 transcript variant 2 NM_001253912.1:c.417+12094= NM_001253912.1:c.417+12094C>T
TBC1D1 transcript variant 2 NM_001253912.2:c.417+12094= NM_001253912.2:c.417+12094C>T
TBC1D1 transcript variant 1 NM_015173.3:c.417+12094= NM_015173.3:c.417+12094C>T
TBC1D1 transcript variant 1 NM_015173.4:c.417+12094= NM_015173.4:c.417+12094C>T
TBC1D1 transcript variant X4 XM_005262646.1:c.417+12094= XM_005262646.1:c.417+12094C>T
TBC1D1 transcript variant X3 XM_005262646.3:c.417+12094= XM_005262646.3:c.417+12094C>T
TBC1D1 transcript variant X5 XM_005262647.1:c.417+12094= XM_005262647.1:c.417+12094C>T
TBC1D1 transcript variant X4 XM_005262647.3:c.417+12094= XM_005262647.3:c.417+12094C>T
TBC1D1 transcript variant X3 XM_005262648.1:c.417+12094= XM_005262648.1:c.417+12094C>T
TBC1D1 transcript variant X5 XM_005262650.1:c.417+12094= XM_005262650.1:c.417+12094C>T
TBC1D1 transcript variant X1 XM_011513659.2:c.417+12094= XM_011513659.2:c.417+12094C>T
TBC1D1 transcript variant X2 XM_011513660.3:c.417+12094= XM_011513660.3:c.417+12094C>T
TBC1D1 transcript variant X5 XM_011513662.3:c.417+12094= XM_011513662.3:c.417+12094C>T
TBC1D1 transcript variant X6 XM_011513663.3:c.417+12094= XM_011513663.3:c.417+12094C>T
TBC1D1 transcript variant X7 XM_011513664.3:c.417+12094= XM_011513664.3:c.417+12094C>T
TBC1D1 transcript variant X10 XM_011513665.3:c.417+12094= XM_011513665.3:c.417+12094C>T
TBC1D1 transcript variant X11 XM_011513666.3:c.417+12094= XM_011513666.3:c.417+12094C>T
TBC1D1 transcript variant X17 XM_011513668.2:c.417+12094= XM_011513668.2:c.417+12094C>T
TBC1D1 transcript variant X8 XM_017007918.2:c.417+12094= XM_017007918.2:c.417+12094C>T
TBC1D1 transcript variant X9 XM_017007919.2:c.417+12094= XM_017007919.2:c.417+12094C>T
TBC1D1 transcript variant X12 XM_017007920.2:c.417+12094= XM_017007920.2:c.417+12094C>T
TBC1D1 transcript variant X15 XM_017007922.1:c.417+12094= XM_017007922.1:c.417+12094C>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#.

31 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss10188858 Jul 11, 2003 (116)
2 AFFY ss76700721 Dec 06, 2007 (129)
3 HGSV ss85709277 Dec 15, 2007 (130)
4 KRIBB_YJKIM ss104936083 Feb 05, 2009 (130)
5 1000GENOMES ss220863790 Jul 14, 2010 (132)
6 ILLUMINA ss244306774 Jul 04, 2010 (132)
7 ILLUMINA ss482295358 May 04, 2012 (137)
8 ILLUMINA ss484811819 May 04, 2012 (137)
9 ILLUMINA ss534583620 Sep 08, 2015 (146)
10 TISHKOFF ss557442188 Apr 25, 2013 (138)
11 ILLUMINA ss779983539 Sep 08, 2015 (146)
12 ILLUMINA ss781714193 Sep 08, 2015 (146)
13 ILLUMINA ss835462852 Sep 08, 2015 (146)
14 EVA-GONL ss979990409 Aug 21, 2014 (142)
15 1000GENOMES ss1309257925 Aug 21, 2014 (142)
16 DDI ss1429842572 Apr 01, 2015 (144)
17 WEILL_CORNELL_DGM ss1923221687 Feb 12, 2016 (147)
18 JJLAB ss2022194350 Sep 14, 2016 (149)
19 HUMAN_LONGEVITY ss2262102018 Dec 20, 2016 (150)
20 TOPMED ss2429618966 Dec 20, 2016 (150)
21 ILLUMINA ss2634106775 Nov 08, 2017 (151)
22 GNOMAD ss2807920698 Nov 08, 2017 (151)
23 TOPMED ss3425596061 Nov 08, 2017 (151)
24 ILLUMINA ss3628943476 Oct 12, 2018 (152)
25 ILLUMINA ss3632044240 Oct 12, 2018 (152)
26 ILLUMINA ss3642329461 Oct 12, 2018 (152)
27 EGCUT_WGS ss3662393792 Jul 13, 2019 (153)
28 EVA_DECODE ss3711817208 Jul 13, 2019 (153)
29 KHV_HUMAN_GENOMES ss3804790420 Jul 13, 2019 (153)
30 SGDP_PRJ ss3858660370 Apr 26, 2020 (154)
31 TOPMED ss4609818366 Apr 26, 2021 (155)
32 1000Genomes NC_000004.11 - 37916227 Oct 12, 2018 (152)
33 Chileans NC_000004.11 - 37916227 Apr 26, 2020 (154)
34 Genetic variation in the Estonian population NC_000004.11 - 37916227 Oct 12, 2018 (152)
35 gnomAD - Genomes NC_000004.12 - 37914606 Apr 26, 2021 (155)
36 Genome of the Netherlands Release 5 NC_000004.11 - 37916227 Apr 26, 2020 (154)
37 HapMap NC_000004.12 - 37914606 Apr 26, 2020 (154)
38 Qatari NC_000004.11 - 37916227 Apr 26, 2020 (154)
39 SGDP_PRJ NC_000004.11 - 37916227 Apr 26, 2020 (154)
40 TopMed NC_000004.12 - 37914606 Apr 26, 2021 (155)
41 ALFA NC_000004.12 - 37914606 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)
rs59723146 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss85709277 NC_000004.9:37738792:C:T NC_000004.12:37914605:C:T (self)
ss484811819 NC_000004.10:37592621:C:T NC_000004.12:37914605:C:T (self)
20636025, 313738, 8132040, 5066287, 5263617, 10677350, ss220863790, ss482295358, ss534583620, ss557442188, ss779983539, ss781714193, ss835462852, ss979990409, ss1309257925, ss1429842572, ss1923221687, ss2022194350, ss2429618966, ss2634106775, ss2807920698, ss3628943476, ss3632044240, ss3642329461, ss3662393792, ss3858660370 NC_000004.11:37916226:C:T NC_000004.12:37914605:C:T (self)
146117098, 2595430, 279537054, 447195922, 11958700615, ss2262102018, ss3425596061, ss3711817208, ss3804790420, ss4609818366 NC_000004.12:37914605:C:T NC_000004.12:37914605:C:T (self)
ss10188858 NT_016297.14:5064869:C:T NC_000004.12:37914605:C:T (self)
ss76700721, ss104936083, ss244306774 NT_016297.16:5075588:C:T NC_000004.12:37914605: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.

1 citation for rs6858735
PMID Title Author Year Journal
23719301 Gene-centric association study of acute chest syndrome and painful crisis in sickle cell disease patients. Galarneau G et al. 2013 Blood
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.post629+eb05767