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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.

rs74046642

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:1185114 (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=0.002675 (708/264690, TOPMED)
A=0.000692 (172/248630, GnomAD_exome)
A=0.000340 (57/167432, ALFA) (+ 8 more)
A=0.002930 (411/140284, GnomAD)
A=0.000783 (93/118802, ExAC)
A=0.00401 (315/78516, PAGE_STUDY)
A=0.00246 (32/13006, GO-ESP)
A=0.0028 (14/5008, 1000G)
A=0.0007 (2/2920, KOREAN)
A=0.0005 (1/1832, Korea1K)
A=0.005 (1/216, Qatari)
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.1185114G>A
GRCh37.p13 chr 1 NC_000001.10:g.1120494G>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+5G>A N/A Intron Variant
TTLL10 transcript variant 3 NM_001371649.1:c.1401+5G>A N/A Intron Variant
TTLL10 transcript variant 2 NM_153254.3:c.1187G>A R [CGT] > H [CAT] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform 2 NP_694986.2:p.Arg396His R (Arg) > H (His) Missense Variant
TTLL10 transcript variant X10 XM_005244738.1:c.1182+5G>A N/A Intron Variant
TTLL10 transcript variant X7 XM_011541177.2:c.1401+5G>A N/A Intron Variant
TTLL10 transcript variant X1 XM_017000906.1:c.1320+5G>A N/A Intron Variant
TTLL10 transcript variant X2 XM_017000907.1:c.1401+5G>A N/A Intron Variant
TTLL10 transcript variant X3 XM_017000908.1:c.1401+5G>A N/A Intron Variant
TTLL10 transcript variant X4 XM_017000909.1:c.1401+5G>A N/A Intron Variant
TTLL10 transcript variant X5 XM_017000910.2:c.1401+5G>A N/A Intron Variant
TTLL10 transcript variant X6 XM_017000911.1:c.1401+5G>A N/A Intron Variant
TTLL10 transcript variant X8 XM_017000912.1:c.1401+5G>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 167432 G=0.999660 A=0.000340
European Sub 144342 G=0.999945 A=0.000055
African Sub 4358 G=0.9906 A=0.0094
African Others Sub 168 G=0.994 A=0.006
African American Sub 4190 G=0.9905 A=0.0095
Asian Sub 6292 G=0.9994 A=0.0006
East Asian Sub 4476 G=0.9991 A=0.0009
Other Asian Sub 1816 G=1.0000 A=0.0000
Latin American 1 Sub 796 G=0.999 A=0.001
Latin American 2 Sub 966 G=1.000 A=0.000
South Asian Sub 280 G=1.000 A=0.000
Other Sub 10398 G=0.99971 A=0.00029


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=0.997325 A=0.002675
gnomAD - Exomes Global Study-wide 248630 G=0.999308 A=0.000692
gnomAD - Exomes European Sub 133438 G=0.999970 A=0.000030
gnomAD - Exomes Asian Sub 48874 G=0.99994 A=0.00006
gnomAD - Exomes American Sub 34142 G=0.99933 A=0.00067
gnomAD - Exomes African Sub 16134 G=0.99138 A=0.00862
gnomAD - Exomes Ashkenazi Jewish Sub 9976 G=1.0000 A=0.0000
gnomAD - Exomes Other Sub 6066 G=0.9995 A=0.0005
gnomAD - Genomes Global Study-wide 140284 G=0.997070 A=0.002930
gnomAD - Genomes European Sub 75956 G=0.99993 A=0.00007
gnomAD - Genomes African Sub 42058 G=0.99082 A=0.00918
gnomAD - Genomes American Sub 13658 G=0.99876 A=0.00124
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=0.9986 A=0.0014
ExAC Global Study-wide 118802 G=0.999217 A=0.000783
ExAC Europe Sub 71370 G=0.99996 A=0.00004
ExAC Asian Sub 24894 G=0.99996 A=0.00004
ExAC American Sub 11462 G=0.99965 A=0.00035
ExAC African Sub 10214 G=0.99178 A=0.00822
ExAC Other Sub 862 G=0.999 A=0.001
The PAGE Study Global Study-wide 78516 G=0.99599 A=0.00401
The PAGE Study AfricanAmerican Sub 32368 G=0.99184 A=0.00816
The PAGE Study Mexican Sub 10810 G=0.99926 A=0.00074
The PAGE Study Asian Sub 8304 G=0.9999 A=0.0001
The PAGE Study PuertoRican Sub 7916 G=0.9979 A=0.0021
The PAGE Study NativeHawaiian Sub 4516 G=0.9998 A=0.0002
The PAGE Study Cuban Sub 4228 G=0.9979 A=0.0021
The PAGE Study Dominican Sub 3826 G=0.9971 A=0.0029
The PAGE Study CentralAmerican Sub 2450 G=0.9996 A=0.0004
The PAGE Study SouthAmerican Sub 1982 G=0.9985 A=0.0015
The PAGE Study NativeAmerican Sub 1260 G=1.0000 A=0.0000
The PAGE Study SouthAsian Sub 856 G=1.000 A=0.000
GO Exome Sequencing Project Global Study-wide 13006 G=0.99754 A=0.00246
GO Exome Sequencing Project European American Sub 8600 G=1.0000 A=0.0000
GO Exome Sequencing Project African American Sub 4406 G=0.9927 A=0.0073
1000Genomes Global Study-wide 5008 G=0.9972 A=0.0028
1000Genomes African Sub 1322 G=0.9909 A=0.0091
1000Genomes East Asian Sub 1008 G=0.9990 A=0.0010
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=0.999 A=0.001
KOREAN population from KRGDB KOREAN Study-wide 2920 G=0.9993 A=0.0007
Korean Genome Project KOREAN Study-wide 1832 G=0.9995 A=0.0005
Qatari Global Study-wide 216 G=0.995 A=0.005
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.1185114= NC_000001.11:g.1185114G>A
GRCh37.p13 chr 1 NC_000001.10:g.1120494= NC_000001.10:g.1120494G>A
TTLL10 transcript variant 2 NM_153254.3:c.1187= NM_153254.3:c.1187G>A
TTLL10 transcript variant 2 NM_153254.2:c.1187= NM_153254.2:c.1187G>A
inactive polyglycylase TTLL10 isoform 2 NP_694986.2:p.Arg396= NP_694986.2:p.Arg396His
TTLL10 transcript variant 1 NM_001130045.1:c.1401+5= NM_001130045.1:c.1401+5G>A
TTLL10 transcript variant 1 NM_001130045.2:c.1401+5= NM_001130045.2:c.1401+5G>A
TTLL10 transcript variant 3 NM_001371649.1:c.1401+5= NM_001371649.1:c.1401+5G>A
TTLL10 transcript variant X1 XM_005244737.1:c.1401+5= XM_005244737.1:c.1401+5G>A
TTLL10 transcript variant X10 XM_005244738.1:c.1182+5= XM_005244738.1:c.1182+5G>A
TTLL10 transcript variant X7 XM_011541177.2:c.1401+5= XM_011541177.2:c.1401+5G>A
TTLL10 transcript variant X1 XM_017000906.1:c.1320+5= XM_017000906.1:c.1320+5G>A
TTLL10 transcript variant X2 XM_017000907.1:c.1401+5= XM_017000907.1:c.1401+5G>A
TTLL10 transcript variant X3 XM_017000908.1:c.1401+5= XM_017000908.1:c.1401+5G>A
TTLL10 transcript variant X4 XM_017000909.1:c.1401+5= XM_017000909.1:c.1401+5G>A
TTLL10 transcript variant X5 XM_017000910.2:c.1401+5= XM_017000910.2:c.1401+5G>A
TTLL10 transcript variant X6 XM_017000911.1:c.1401+5= XM_017000911.1:c.1401+5G>A
TTLL10 transcript variant X8 XM_017000912.1:c.1401+5= XM_017000912.1:c.1401+5G>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#.

45 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 ILLUMINA-UK ss118440636 Feb 14, 2009 (130)
2 SEATTLESEQ ss159695686 Dec 01, 2009 (131)
3 ILLUMINA ss161037388 Dec 01, 2009 (131)
4 BUSHMAN ss197889704 Jul 04, 2010 (132)
5 1000GENOMES ss217405761 Jul 14, 2010 (132)
6 1000GENOMES ss217410913 Jul 14, 2010 (132)
7 1000GENOMES ss218192294 Jul 14, 2010 (132)
8 NHLBI-ESP ss341924453 May 09, 2011 (134)
9 ILLUMINA ss479212158 Sep 08, 2015 (146)
10 1000GENOMES ss489714636 May 04, 2012 (137)
11 EXOME_CHIP ss491284083 May 04, 2012 (137)
12 ILLUMINA ss780767413 Sep 08, 2015 (146)
13 ILLUMINA ss783446818 Sep 08, 2015 (146)
14 1000GENOMES ss1289353178 Aug 21, 2014 (142)
15 EVA_EXAC ss1685226090 Apr 01, 2015 (144)
16 ILLUMINA ss1751863635 Sep 08, 2015 (146)
17 ILLUMINA ss1917721010 Feb 12, 2016 (147)
18 WEILL_CORNELL_DGM ss1917964784 Feb 12, 2016 (147)
19 ILLUMINA ss1945981844 Feb 12, 2016 (147)
20 ILLUMINA ss1958230936 Feb 12, 2016 (147)
21 HUMAN_LONGEVITY ss2159391952 Dec 20, 2016 (150)
22 TOPMED ss2321531162 Dec 20, 2016 (150)
23 GNOMAD ss2731000426 Nov 08, 2017 (151)
24 GNOMAD ss2746174415 Nov 08, 2017 (151)
25 GNOMAD ss2750679730 Nov 08, 2017 (151)
26 AFFY ss2984841299 Nov 08, 2017 (151)
27 ILLUMINA ss3021043890 Nov 08, 2017 (151)
28 TOPMED ss3066489041 Nov 08, 2017 (151)
29 ILLUMINA ss3626007229 Oct 11, 2018 (152)
30 ILLUMINA ss3634302115 Oct 11, 2018 (152)
31 ILLUMINA ss3635978744 Oct 11, 2018 (152)
32 ILLUMINA ss3640009481 Oct 11, 2018 (152)
33 ILLUMINA ss3644477708 Oct 11, 2018 (152)
34 ILLUMINA ss3651365945 Oct 11, 2018 (152)
35 ILLUMINA ss3653615065 Oct 11, 2018 (152)
36 ILLUMINA ss3724988545 Jul 12, 2019 (153)
37 ILLUMINA ss3744337438 Jul 12, 2019 (153)
38 ILLUMINA ss3744603046 Jul 12, 2019 (153)
39 EVA ss3745725125 Jul 12, 2019 (153)
40 PAGE_CC ss3770778905 Jul 12, 2019 (153)
41 ILLUMINA ss3772104803 Jul 12, 2019 (153)
42 EVA ss3823543139 Apr 25, 2020 (154)
43 KRGDB ss3892848918 Apr 25, 2020 (154)
44 KOGIC ss3943637877 Apr 25, 2020 (154)
45 TOPMED ss4436540795 Apr 25, 2021 (155)
46 1000Genomes NC_000001.10 - 1120494 Oct 11, 2018 (152)
47 ExAC NC_000001.10 - 1120494 Oct 11, 2018 (152)
48 gnomAD - Genomes NC_000001.11 - 1185114 Apr 25, 2021 (155)
49 gnomAD - Exomes NC_000001.10 - 1120494 Jul 12, 2019 (153)
50 GO Exome Sequencing Project NC_000001.10 - 1120494 Oct 11, 2018 (152)
51 KOREAN population from KRGDB NC_000001.10 - 1120494 Apr 25, 2020 (154)
52 Korean Genome Project NC_000001.11 - 1185114 Apr 25, 2020 (154)
53 The PAGE Study NC_000001.11 - 1185114 Jul 12, 2019 (153)
54 Qatari NC_000001.10 - 1120494 Apr 25, 2020 (154)
55 TopMed NC_000001.11 - 1185114 Apr 25, 2021 (155)
56 ALFA NC_000001.11 - 1185114 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
ss118440636, ss197889704, ss217405761, ss217410913 NC_000001.9:1110356:G:A NC_000001.11:1185113:G:A (self)
18363, 4399780, 15273, 1876, 26312, 6714, ss218192294, ss341924453, ss479212158, ss489714636, ss491284083, ss780767413, ss783446818, ss1289353178, ss1685226090, ss1751863635, ss1917721010, ss1917964784, ss1945981844, ss1958230936, ss2321531162, ss2731000426, ss2746174415, ss2750679730, ss2984841299, ss3021043890, ss3626007229, ss3634302115, ss3635978744, ss3640009481, ss3644477708, ss3651365945, ss3653615065, ss3744337438, ss3744603046, ss3745725125, ss3772104803, ss3823543139, ss3892848918 NC_000001.10:1120493:G:A NC_000001.11:1185113:G:A (self)
160073, 15878, 374, 84515, 147130, 6263756567, ss2159391952, ss3066489041, ss3724988545, ss3770778905, ss3943637877, ss4436540795 NC_000001.11:1185113:G:A NC_000001.11:1185113:G:A (self)
ss159695686, ss161037388 NT_004350.19:599125:G:A NC_000001.11:1185113: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 rs74046642

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