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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.

rs116251234

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:1185123 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.019702 (5215/264690, TOPMED)
A=0.004674 (1156/247348, GnomAD_exome)
A=0.001731 (345/199278, ALFA) (+ 8 more)
A=0.018897 (2651/140288, GnomAD)
A=0.005973 (708/118536, ExAC)
A=0.02821 (2219/78668, PAGE_STUDY)
A=0.02168 (282/13006, GO-ESP)
A=0.0216 (108/5008, 1000G)
A=0.005 (1/216, Qatari)
G=0.5 (4/8, SGDP_PRJ)
A=0.5 (4/8, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TTLL10 : Missense 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 1 NC_000001.11:g.1185123G>A
GRCh37.p13 chr 1 NC_000001.10:g.1120503G>A
Gene: TTLL10, tubulin tyrosine ligase like 10 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TTLL10 transcript variant 1 NM_001130045.2:c.1401+14G…

NM_001130045.2:c.1401+14G>A

N/A Intron Variant
TTLL10 transcript variant 3 NM_001371649.1:c.1401+14G…

NM_001371649.1:c.1401+14G>A

N/A Intron Variant
TTLL10 transcript variant 2 NM_153254.3:c.1196G>A C [TGC] > Y [TAC] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform 2 NP_694986.2:p.Cys399Tyr C (Cys) > Y (Tyr) Missense Variant
TTLL10 transcript variant X10 XM_005244738.1:c.1182+14G…

XM_005244738.1:c.1182+14G>A

N/A Intron Variant
TTLL10 transcript variant X7 XM_011541177.2:c.1401+14G…

XM_011541177.2:c.1401+14G>A

N/A Intron Variant
TTLL10 transcript variant X1 XM_017000906.1:c.1320+14G…

XM_017000906.1:c.1320+14G>A

N/A Intron Variant
TTLL10 transcript variant X2 XM_017000907.1:c.1401+14G…

XM_017000907.1:c.1401+14G>A

N/A Intron Variant
TTLL10 transcript variant X3 XM_017000908.1:c.1401+14G…

XM_017000908.1:c.1401+14G>A

N/A Intron Variant
TTLL10 transcript variant X4 XM_017000909.1:c.1401+14G…

XM_017000909.1:c.1401+14G>A

N/A Intron Variant
TTLL10 transcript variant X5 XM_017000910.2:c.1401+14G…

XM_017000910.2:c.1401+14G>A

N/A Intron Variant
TTLL10 transcript variant X6 XM_017000911.1:c.1401+14G…

XM_017000911.1:c.1401+14G>A

N/A Intron Variant
TTLL10 transcript variant X8 XM_017000912.1:c.1401+14G…

XM_017000912.1:c.1401+14G>A

N/A Intron Variant
TTLL10 transcript variant X9 XR_001737088.1:n. N/A Intron Variant
TTLL10 transcript variant X11 XR_001737089.1:n. N/A Genic Downstream 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

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 199278 G=0.998269 A=0.001731
European Sub 169924 G=0.999929 A=0.000071
African Sub 4966 G=0.9436 A=0.0564
African Others Sub 176 G=0.938 A=0.062
African American Sub 4790 G=0.9438 A=0.0562
Asian Sub 6348 G=1.0000 A=0.0000
East Asian Sub 4502 G=1.0000 A=0.0000
Other Asian Sub 1846 G=1.0000 A=0.0000
Latin American 1 Sub 796 G=0.984 A=0.016
Latin American 2 Sub 966 G=0.996 A=0.004
South Asian Sub 280 G=1.000 A=0.000
Other Sub 15998 G=0.99775 A=0.00225


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 G=0.980298 A=0.019702
gnomAD - Exomes Global Study-wide 247348 G=0.995326 A=0.004674
gnomAD - Exomes European Sub 132796 G=0.999895 A=0.000105
gnomAD - Exomes Asian Sub 48726 G=0.99996 A=0.00004
gnomAD - Exomes American Sub 33774 G=0.99674 A=0.00326
gnomAD - Exomes African Sub 16118 G=0.93703 A=0.06297
gnomAD - Exomes Ashkenazi Jewish Sub 9902 G=1.0000 A=0.0000
gnomAD - Exomes Other Sub 6032 G=0.9975 A=0.0025
gnomAD - Genomes Global Study-wide 140288 G=0.981103 A=0.018897
gnomAD - Genomes European Sub 75962 G=0.99987 A=0.00013
gnomAD - Genomes African Sub 42052 G=0.94019 A=0.05981
gnomAD - Genomes American Sub 13662 G=0.99341 A=0.00659
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2154 G=0.9833 A=0.0167
ExAC Global Study-wide 118536 G=0.994027 A=0.005973
ExAC Europe Sub 71212 G=0.99994 A=0.00006
ExAC Asian Sub 24806 G=1.00000 A=0.00000
ExAC American Sub 11458 G=0.99738 A=0.00262
ExAC African Sub 10202 G=0.93423 A=0.06577
ExAC Other Sub 858 G=0.997 A=0.003
The PAGE Study Global Study-wide 78668 G=0.97179 A=0.02821
The PAGE Study AfricanAmerican Sub 32492 G=0.94352 A=0.05648
The PAGE Study Mexican Sub 10808 G=0.99704 A=0.00296
The PAGE Study Asian Sub 8318 G=1.0000 A=0.0000
The PAGE Study PuertoRican Sub 7916 G=0.9836 A=0.0164
The PAGE Study NativeHawaiian Sub 4534 G=0.9989 A=0.0011
The PAGE Study Cuban Sub 4226 G=0.9891 A=0.0109
The PAGE Study Dominican Sub 3826 G=0.9699 A=0.0301
The PAGE Study CentralAmerican Sub 2450 G=0.9890 A=0.0110
The PAGE Study SouthAmerican Sub 1982 G=0.9939 A=0.0061
The PAGE Study NativeAmerican Sub 1260 G=0.9865 A=0.0135
The PAGE Study SouthAsian Sub 856 G=1.000 A=0.000
GO Exome Sequencing Project Global Study-wide 13006 G=0.97832 A=0.02168
GO Exome Sequencing Project European American Sub 8600 G=1.0000 A=0.0000
GO Exome Sequencing Project African American Sub 4406 G=0.9360 A=0.0640
1000Genomes Global Study-wide 5008 G=0.9784 A=0.0216
1000Genomes African Sub 1322 G=0.9221 A=0.0779
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=0.993 A=0.007
Qatari Global Study-wide 216 G=0.995 A=0.005
SGDP_PRJ Global Study-wide 8 G=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 G= A
GRCh38.p13 chr 1 NC_000001.11:g.1185123= NC_000001.11:g.1185123G>A
GRCh37.p13 chr 1 NC_000001.10:g.1120503= NC_000001.10:g.1120503G>A
TTLL10 transcript variant 2 NM_153254.3:c.1196= NM_153254.3:c.1196G>A
TTLL10 transcript variant 2 NM_153254.2:c.1196= NM_153254.2:c.1196G>A
inactive polyglycylase TTLL10 isoform 2 NP_694986.2:p.Cys399= NP_694986.2:p.Cys399Tyr
TTLL10 transcript variant 1 NM_001130045.1:c.1401+14= NM_001130045.1:c.1401+14G>A
TTLL10 transcript variant 1 NM_001130045.2:c.1401+14= NM_001130045.2:c.1401+14G>A
TTLL10 transcript variant 3 NM_001371649.1:c.1401+14= NM_001371649.1:c.1401+14G>A
TTLL10 transcript variant X1 XM_005244737.1:c.1401+14= XM_005244737.1:c.1401+14G>A
TTLL10 transcript variant X10 XM_005244738.1:c.1182+14= XM_005244738.1:c.1182+14G>A
TTLL10 transcript variant X7 XM_011541177.2:c.1401+14= XM_011541177.2:c.1401+14G>A
TTLL10 transcript variant X1 XM_017000906.1:c.1320+14= XM_017000906.1:c.1320+14G>A
TTLL10 transcript variant X2 XM_017000907.1:c.1401+14= XM_017000907.1:c.1401+14G>A
TTLL10 transcript variant X3 XM_017000908.1:c.1401+14= XM_017000908.1:c.1401+14G>A
TTLL10 transcript variant X4 XM_017000909.1:c.1401+14= XM_017000909.1:c.1401+14G>A
TTLL10 transcript variant X5 XM_017000910.2:c.1401+14= XM_017000910.2:c.1401+14G>A
TTLL10 transcript variant X6 XM_017000911.1:c.1401+14= XM_017000911.1:c.1401+14G>A
TTLL10 transcript variant X8 XM_017000912.1:c.1401+14= XM_017000912.1:c.1401+14G>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#.

41 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss217405773 Jul 14, 2010 (132)
2 1000GENOMES ss217410925 Jul 14, 2010 (132)
3 1000GENOMES ss328360008 May 09, 2011 (134)
4 NHLBI-ESP ss341924458 May 09, 2011 (134)
5 1000GENOMES ss489714640 May 04, 2012 (137)
6 EXOME_CHIP ss491284085 May 04, 2012 (137)
7 TISHKOFF ss553714426 Apr 25, 2013 (138)
8 ILLUMINA ss780767825 Sep 08, 2015 (146)
9 ILLUMINA ss783447249 Sep 08, 2015 (146)
10 1000GENOMES ss1289353180 Aug 21, 2014 (142)
11 EVA_EXAC ss1685226093 Apr 01, 2015 (144)
12 ILLUMINA ss1751863636 Sep 08, 2015 (146)
13 ILLUMINA ss1917721011 Feb 12, 2016 (147)
14 WEILL_CORNELL_DGM ss1917964786 Feb 12, 2016 (147)
15 ILLUMINA ss1945981845 Feb 12, 2016 (147)
16 ILLUMINA ss1958230937 Feb 12, 2016 (147)
17 HUMAN_LONGEVITY ss2159391954 Dec 20, 2016 (150)
18 TOPMED ss2321531165 Dec 20, 2016 (150)
19 GNOMAD ss2731000430 Nov 08, 2017 (151)
20 GNOMAD ss2746174417 Nov 08, 2017 (151)
21 GNOMAD ss2750679732 Nov 08, 2017 (151)
22 AFFY ss2984841300 Nov 08, 2017 (151)
23 ILLUMINA ss3021043891 Nov 08, 2017 (151)
24 TOPMED ss3066489044 Nov 08, 2017 (151)
25 ILLUMINA ss3626007230 Oct 11, 2018 (152)
26 ILLUMINA ss3634302116 Oct 11, 2018 (152)
27 ILLUMINA ss3640009482 Oct 11, 2018 (152)
28 ILLUMINA ss3644477709 Oct 11, 2018 (152)
29 ILLUMINA ss3651365946 Oct 11, 2018 (152)
30 ILLUMINA ss3653615066 Oct 11, 2018 (152)
31 ILLUMINA ss3724988546 Jul 12, 2019 (153)
32 ILLUMINA ss3744337439 Jul 12, 2019 (153)
33 ILLUMINA ss3744603047 Jul 12, 2019 (153)
34 PAGE_CC ss3770778906 Jul 12, 2019 (153)
35 ILLUMINA ss3772104804 Jul 12, 2019 (153)
36 KHV_HUMAN_GENOMES ss3798747780 Jul 12, 2019 (153)
37 EVA ss3823543141 Apr 25, 2020 (154)
38 EVA ss3825982913 Apr 25, 2020 (154)
39 SGDP_PRJ ss3848005959 Apr 25, 2020 (154)
40 EVA ss3986091340 Apr 25, 2021 (155)
41 TOPMED ss4436540799 Apr 25, 2021 (155)
42 1000Genomes NC_000001.10 - 1120503 Oct 11, 2018 (152)
43 ExAC NC_000001.10 - 1120503 Oct 11, 2018 (152)
44 gnomAD - Genomes NC_000001.11 - 1185123 Apr 25, 2021 (155)
45 gnomAD - Exomes NC_000001.10 - 1120503 Jul 12, 2019 (153)
46 GO Exome Sequencing Project NC_000001.10 - 1120503 Oct 11, 2018 (152)
47 The PAGE Study NC_000001.11 - 1185123 Jul 12, 2019 (153)
48 Qatari NC_000001.10 - 1120503 Apr 25, 2020 (154)
49 SGDP_PRJ NC_000001.10 - 1120503 Apr 25, 2020 (154)
50 TopMed NC_000001.11 - 1185123 Apr 25, 2021 (155)
51 ALFA NC_000001.11 - 1185123 Apr 25, 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
ss217405773, ss217410925 NC_000001.9:1110365:G:A NC_000001.11:1185122:G:A (self)
18365, 4399783, 15277, 1878, 6716, 22939, ss328360008, ss341924458, ss489714640, ss491284085, ss553714426, ss780767825, ss783447249, ss1289353180, ss1685226093, ss1751863636, ss1917721011, ss1917964786, ss1945981845, ss1958230937, ss2321531165, ss2731000430, ss2746174417, ss2750679732, ss2984841300, ss3021043891, ss3626007230, ss3634302116, ss3640009482, ss3644477709, ss3651365946, ss3653615066, ss3744337439, ss3744603047, ss3772104804, ss3823543141, ss3825982913, ss3848005959, ss3986091340 NC_000001.10:1120502:G:A NC_000001.11:1185122:G:A (self)
160077, 375, 84518, 147134, 14608709431, ss2159391954, ss3066489044, ss3724988546, ss3770778906, ss3798747780, ss4436540799 NC_000001.11:1185122:G:A NC_000001.11:1185122:G:A (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 rs116251234

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