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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.

rs77026477

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:1185115 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.011719 (3102/264690, TOPMED)
C=0.002926 (727/248498, GnomAD_exome)
C=0.010931 (1533/140248, GnomAD) (+ 6 more)
C=0.003670 (436/118804, ExAC)
C=0.00377 (184/48772, ALFA)
C=0.01299 (169/13006, GO-ESP)
C=0.0120 (60/5008, 1000G)
C=0.019 (4/216, Qatari)
T=0.39 (7/18, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TTLL10 : Synonymous 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.1185115T>C
GRCh37.p13 chr 1 NC_000001.10:g.1120495T>C
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+6T>C N/A Intron Variant
TTLL10 transcript variant 3 NM_001371649.1:c.1401+6T>C N/A Intron Variant
TTLL10 transcript variant 2 NM_153254.3:c.1188T>C R [CGT] > R [CGC] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform 2 NP_694986.2:p.Arg396= R (Arg) > R (Arg) Synonymous Variant
TTLL10 transcript variant X10 XM_005244738.1:c.1182+6T>C N/A Intron Variant
TTLL10 transcript variant X7 XM_011541177.2:c.1401+6T>C N/A Intron Variant
TTLL10 transcript variant X1 XM_017000906.1:c.1320+6T>C N/A Intron Variant
TTLL10 transcript variant X2 XM_017000907.1:c.1401+6T>C N/A Intron Variant
TTLL10 transcript variant X3 XM_017000908.1:c.1401+6T>C N/A Intron Variant
TTLL10 transcript variant X4 XM_017000909.1:c.1401+6T>C N/A Intron Variant
TTLL10 transcript variant X5 XM_017000910.2:c.1401+6T>C N/A Intron Variant
TTLL10 transcript variant X6 XM_017000911.1:c.1401+6T>C N/A Intron Variant
TTLL10 transcript variant X8 XM_017000912.1:c.1401+6T>C 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 48772 T=0.99623 C=0.00377
European Sub 34012 T=0.99912 C=0.00088
African Sub 3876 T=0.9685 C=0.0315
African Others Sub 122 T=0.967 C=0.033
African American Sub 3754 T=0.9686 C=0.0314
Asian Sub 190 T=1.000 C=0.000
East Asian Sub 130 T=1.000 C=0.000
Other Asian Sub 60 T=1.00 C=0.00
Latin American 1 Sub 516 T=0.986 C=0.014
Latin American 2 Sub 662 T=0.998 C=0.002
South Asian Sub 114 T=1.000 C=0.000
Other Sub 9402 T=0.9974 C=0.0026


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=0.988281 C=0.011719
gnomAD - Exomes Global Study-wide 248498 T=0.997074 C=0.002926
gnomAD - Exomes European Sub 133426 T=0.999828 C=0.000172
gnomAD - Exomes Asian Sub 48828 T=0.99994 C=0.00006
gnomAD - Exomes American Sub 34084 T=0.99789 C=0.00211
gnomAD - Exomes African Sub 16126 T=0.96490 C=0.03510
gnomAD - Exomes Ashkenazi Jewish Sub 9974 T=0.9955 C=0.0045
gnomAD - Exomes Other Sub 6060 T=0.9970 C=0.0030
gnomAD - Genomes Global Study-wide 140248 T=0.989069 C=0.010931
gnomAD - Genomes European Sub 75946 T=0.99974 C=0.00026
gnomAD - Genomes African Sub 42030 T=0.96652 C=0.03348
gnomAD - Genomes American Sub 13662 T=0.99524 C=0.00476
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.9958 C=0.0042
gnomAD - Genomes East Asian Sub 3134 T=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2152 T=0.9875 C=0.0125
ExAC Global Study-wide 118804 T=0.996330 C=0.003670
ExAC Europe Sub 71370 T=0.99954 C=0.00046
ExAC Asian Sub 24884 T=0.99996 C=0.00004
ExAC American Sub 11464 T=0.99756 C=0.00244
ExAC African Sub 10222 T=0.96371 C=0.03629
ExAC Other Sub 864 T=0.997 C=0.003
GO Exome Sequencing Project Global Study-wide 13006 T=0.98701 C=0.01299
GO Exome Sequencing Project European American Sub 8600 T=0.9997 C=0.0003
GO Exome Sequencing Project African American Sub 4406 T=0.9623 C=0.0377
1000Genomes Global Study-wide 5008 T=0.9880 C=0.0120
1000Genomes African Sub 1322 T=0.9554 C=0.0446
1000Genomes East Asian Sub 1008 T=1.0000 C=0.0000
1000Genomes Europe Sub 1006 T=1.0000 C=0.0000
1000Genomes South Asian Sub 978 T=1.000 C=0.000
1000Genomes American Sub 694 T=0.999 C=0.001
Qatari Global Study-wide 216 T=0.981 C=0.019
SGDP_PRJ Global Study-wide 18 T=0.39 C=0.61
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= C
GRCh38.p13 chr 1 NC_000001.11:g.1185115= NC_000001.11:g.1185115T>C
GRCh37.p13 chr 1 NC_000001.10:g.1120495= NC_000001.10:g.1120495T>C
TTLL10 transcript variant 2 NM_153254.3:c.1188= NM_153254.3:c.1188T>C
TTLL10 transcript variant 2 NM_153254.2:c.1188= NM_153254.2:c.1188T>C
inactive polyglycylase TTLL10 isoform 2 NP_694986.2:p.Arg396= NP_694986.2:p.Arg396=
TTLL10 transcript variant 1 NM_001130045.1:c.1401+6= NM_001130045.1:c.1401+6T>C
TTLL10 transcript variant 1 NM_001130045.2:c.1401+6= NM_001130045.2:c.1401+6T>C
TTLL10 transcript variant 3 NM_001371649.1:c.1401+6= NM_001371649.1:c.1401+6T>C
TTLL10 transcript variant X1 XM_005244737.1:c.1401+6= XM_005244737.1:c.1401+6T>C
TTLL10 transcript variant X10 XM_005244738.1:c.1182+6= XM_005244738.1:c.1182+6T>C
TTLL10 transcript variant X7 XM_011541177.2:c.1401+6= XM_011541177.2:c.1401+6T>C
TTLL10 transcript variant X1 XM_017000906.1:c.1320+6= XM_017000906.1:c.1320+6T>C
TTLL10 transcript variant X2 XM_017000907.1:c.1401+6= XM_017000907.1:c.1401+6T>C
TTLL10 transcript variant X3 XM_017000908.1:c.1401+6= XM_017000908.1:c.1401+6T>C
TTLL10 transcript variant X4 XM_017000909.1:c.1401+6= XM_017000909.1:c.1401+6T>C
TTLL10 transcript variant X5 XM_017000910.2:c.1401+6= XM_017000910.2:c.1401+6T>C
TTLL10 transcript variant X6 XM_017000911.1:c.1401+6= XM_017000911.1:c.1401+6T>C
TTLL10 transcript variant X8 XM_017000912.1:c.1401+6= XM_017000912.1:c.1401+6T>C
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#.

27 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 ILLUMINA ss161037389 Dec 01, 2009 (131)
2 BUSHMAN ss197889708 Jul 04, 2010 (132)
3 1000GENOMES ss217405768 Jul 14, 2010 (132)
4 1000GENOMES ss217410919 Jul 14, 2010 (132)
5 1000GENOMES ss218192295 Jul 14, 2010 (132)
6 NHLBI-ESP ss341924456 May 09, 2011 (134)
7 ILLUMINA ss479210666 Sep 08, 2015 (146)
8 1000GENOMES ss489714638 May 04, 2012 (137)
9 TISHKOFF ss553714425 Apr 25, 2013 (138)
10 JMKIDD_LAB ss1067414453 Aug 21, 2014 (142)
11 JMKIDD_LAB ss1067614030 Aug 21, 2014 (142)
12 1000GENOMES ss1289353179 Aug 21, 2014 (142)
13 EVA_EXAC ss1685226091 Apr 01, 2015 (144)
14 WEILL_CORNELL_DGM ss1917964785 Feb 12, 2016 (147)
15 HUMAN_LONGEVITY ss2159391953 Dec 20, 2016 (150)
16 TOPMED ss2321531163 Dec 20, 2016 (150)
17 GNOMAD ss2731000427 Nov 08, 2017 (151)
18 GNOMAD ss2746174416 Nov 08, 2017 (151)
19 GNOMAD ss2750679731 Nov 08, 2017 (151)
20 TOPMED ss3066489042 Nov 08, 2017 (151)
21 ILLUMINA ss3635978745 Oct 11, 2018 (152)
22 KHV_HUMAN_GENOMES ss3798747779 Jul 12, 2019 (153)
23 EVA ss3823543140 Apr 25, 2020 (154)
24 EVA ss3825549335 Apr 25, 2020 (154)
25 SGDP_PRJ ss3848005958 Apr 25, 2020 (154)
26 EVA ss3986091339 Apr 25, 2021 (155)
27 TOPMED ss4436540796 Apr 25, 2021 (155)
28 1000Genomes NC_000001.10 - 1120495 Oct 11, 2018 (152)
29 ExAC NC_000001.10 - 1120495 Oct 11, 2018 (152)
30 gnomAD - Genomes NC_000001.11 - 1185115 Apr 25, 2021 (155)
31 gnomAD - Exomes NC_000001.10 - 1120495 Jul 12, 2019 (153)
32 GO Exome Sequencing Project NC_000001.10 - 1120495 Oct 11, 2018 (152)
33 Qatari NC_000001.10 - 1120495 Apr 25, 2020 (154)
34 SGDP_PRJ NC_000001.10 - 1120495 Apr 25, 2020 (154)
35 TopMed NC_000001.11 - 1185115 Apr 25, 2021 (155)
36 ALFA NC_000001.11 - 1185115 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
ss197889708, ss217405768, ss217410919 NC_000001.9:1110357:T:C NC_000001.11:1185114:T:C (self)
18364, 4399781, 15274, 1877, 6715, 22938, ss218192295, ss341924456, ss479210666, ss489714638, ss553714425, ss1067414453, ss1067614030, ss1289353179, ss1685226091, ss1917964785, ss2321531163, ss2731000427, ss2746174416, ss2750679731, ss3635978745, ss3823543140, ss3825549335, ss3848005958, ss3986091339 NC_000001.10:1120494:T:C NC_000001.11:1185114:T:C (self)
160074, 84516, 147131, 6132872610, ss2159391953, ss3066489042, ss3798747779, ss4436540796 NC_000001.11:1185114:T:C NC_000001.11:1185114:T:C (self)
ss161037389 NT_004350.19:599126:T:C NC_000001.11:1185114:T:C (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 rs77026477

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