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dbSNP Short Genetic Variations

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.

rs55670497

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr6:30153834 (GRCh38.p12) 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=0.03197 (4014/125568, TOPMED)
T=0.0301 (932/30946, GnomAD)
T=0.034 (171/5008, 1000G) (+ 3 more)
T=0.016 (70/4480, Estonian)
T=0.008 (29/3854, ALSPAC)
T=0.010 (38/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TRIM10 : Intron 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.p12 chr 6 NC_000006.12:g.30153834C>T
GRCh37.p13 chr 6 NC_000006.11:g.30121611C>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.1633642C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.1633748C>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.1408963C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.1414559C>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.1409751C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.1415336C>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.1452762C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.1452060C>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.1464556C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.1470176C>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.1497912C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.1503497C>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.2:g.1411930C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.1:g.1361846C>T
Gene: TRIM10, tripartite motif containing 10 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TRIM10 transcript variant 2 NM_052828.2:c. N/A Intron Variant
TRIM10 transcript variant 1 NM_006778.3:c. N/A 3 Prime UTR Variant
TRIM10 transcript variant X4 XM_011514225.1:c. N/A Intron Variant
TRIM10 transcript variant X1 XM_011514221.1:c. N/A 3 Prime UTR Variant
TRIM10 transcript variant X2 XM_011514222.2:c. N/A 3 Prime UTR Variant
TRIM10 transcript variant X3 XM_011514223.2:c. N/A 3 Prime UTR 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

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 125568 C=0.96803 T=0.03197
gnomAD - Genomes Global Study-wide 30946 C=0.9699 T=0.0301
gnomAD - Genomes European Sub 18486 C=0.9852 T=0.0148
gnomAD - Genomes African Sub 8720 C=0.932 T=0.068
gnomAD - Genomes East Asian Sub 1620 C=0.998 T=0.002
gnomAD - Genomes Other Sub 982 C=0.96 T=0.04
gnomAD - Genomes American Sub 836 C=0.97 T=0.03
gnomAD - Genomes Ashkenazi Jewish Sub 302 C=0.97 T=0.03
1000Genomes Global Study-wide 5008 C=0.966 T=0.034
1000Genomes African Sub 1322 C=0.930 T=0.070
1000Genomes East Asian Sub 1008 C=0.997 T=0.003
1000Genomes Europe Sub 1006 C=0.983 T=0.017
1000Genomes South Asian Sub 978 C=0.97 T=0.03
1000Genomes American Sub 694 C=0.96 T=0.04
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.984 T=0.016
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.992 T=0.008
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.990 T=0.010
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 Note
GRCh38.p12 chr 6 NC_000006.12:g.30153834C= NC_000006.12:g.30153834C>T
GRCh37.p13 chr 6 NC_000006.11:g.30121611C= NC_000006.11:g.30121611C>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.1633642C= NT_113891.3:g.1633642C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.1633748C= NT_113891.2:g.1633748C>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.1408963C= NT_167248.2:g.1408963C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.1414559C= NT_167248.1:g.1414559C>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.1409751C= NT_167245.2:g.1409751C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.1415336C= NT_167245.1:g.1415336C>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.1452762C= NT_167249.2:g.1452762C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.1452060C= NT_167249.1:g.1452060C>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.1464556C= NT_167246.2:g.1464556C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.1470176C= NT_167246.1:g.1470176C>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.1497912C= NT_167247.2:g.1497912C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.1503497C= NT_167247.1:g.1503497C>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.2:g.1411930C= NT_167244.2:g.1411930C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.1:g.1361846C= NT_167244.1:g.1361846C>T
TRIM10 transcript variant 1 NM_006778.3:c.*135G= NM_006778.3:c.*135G>A
TRIM10 transcript variant X2 XM_011514222.2:c.*135G= XM_011514222.2:c.*135G>A
TRIM10 transcript variant X3 XM_011514223.2:c.*135G= XM_011514223.2:c.*135G>A
TRIM10 transcript variant X1 XM_011514221.1:c.*135G= XM_011514221.1:c.*135G>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#.

33 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 SI_EXO ss76898269 Dec 06, 2007 (129)
2 HGSV ss84529029 Dec 15, 2007 (130)
3 BUSHMAN ss201597488 Jul 04, 2010 (132)
4 1000GENOMES ss222292003 Jul 14, 2010 (137)
5 1000GENOMES ss240458878 Jul 15, 2010 (137)
6 ILLUMINA ss484132853 May 04, 2012 (137)
7 ILLUMINA ss485225754 May 04, 2012 (137)
8 ILLUMINA ss536322774 Sep 08, 2015 (146)
9 SSMP ss653018911 Apr 25, 2013 (138)
10 ILLUMINA ss779440521 Sep 08, 2015 (146)
11 ILLUMINA ss782511986 Sep 08, 2015 (146)
12 ILLUMINA ss834909963 Sep 08, 2015 (146)
13 EVA-GONL ss982744395 Aug 21, 2014 (142)
14 1000GENOMES ss1319512138 Aug 21, 2014 (142)
15 EVA_GENOME_DK ss1581596259 Apr 01, 2015 (144)
16 EVA_FINRISK ss1584044750 Apr 01, 2015 (144)
17 EVA_DECODE ss1592291755 Apr 01, 2015 (144)
18 EVA_UK10K_ALSPAC ss1615250949 Apr 01, 2015 (144)
19 EVA_UK10K_TWINSUK ss1658244982 Apr 01, 2015 (144)
20 EVA_MGP ss1711118832 Apr 01, 2015 (144)
21 WEILL_CORNELL_DGM ss1925996572 Feb 12, 2016 (147)
22 GENOMED ss1970350400 Jul 19, 2016 (147)
23 JJLAB ss2023626664 Sep 14, 2016 (149)
24 USC_VALOUEV ss2151791946 Nov 08, 2017 (151)
25 HUMAN_LONGEVITY ss2282872328 Dec 20, 2016 (150)
26 TOPMED ss2451242247 Dec 20, 2016 (150)
27 ILLUMINA ss2634424406 Nov 08, 2017 (151)
28 GNOMAD ss2837312771 Nov 08, 2017 (151)
29 SWEGEN ss2998765508 Nov 08, 2017 (151)
30 TOPMED ss3493598238 Nov 08, 2017 (151)
31 ILLUMINA ss3629492406 Oct 12, 2018 (152)
32 ILLUMINA ss3632343605 Oct 12, 2018 (152)
33 OMUKHERJEE_ADBS ss3646333140 Oct 12, 2018 (152)
34 1000Genomes NC_000006.11 - 30121611 Oct 12, 2018 (152)
35 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 30121611 Oct 12, 2018 (152)
36 Genetic variation in the Estonian population NC_000006.11 - 30121611 Oct 12, 2018 (152)
37 gnomAD - Genomes NC_000006.11 - 30121611 Oct 12, 2018 (152)
38 TopMed NC_000006.12 - 30153834 Oct 12, 2018 (152)
39 UK 10K study - Twins NC_000006.11 - 30121611 Oct 12, 2018 (152)
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)
rs59216356 May 25, 2008 (130)
rs115296900 May 04, 2012 (137)
rs117723824 Aug 16, 2010 (132)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss84529029 NC_000006.9:30229589:C= NC_000006.12:30153833:C= (self)
ss201597488, ss485225754, ss1592291755 NC_000006.10:30229589:C= NC_000006.12:30153833:C= (self)
31277546, 17437377, 12426193, 177940528, 17437377, ss222292003, ss240458878, ss484132853, ss536322774, ss653018911, ss779440521, ss782511986, ss834909963, ss982744395, ss1319512138, ss1581596259, ss1584044750, ss1615250949, ss1658244982, ss1711118832, ss1925996572, ss1970350400, ss2023626664, ss2151791946, ss2451242247, ss2634424406, ss2837312771, ss2998765508, ss3629492406, ss3632343605, ss3646333140 NC_000006.11:30121610:C= NC_000006.12:30153833:C= (self)
334861882, ss2282872328, ss3493598238 NC_000006.12:30153833:C= NC_000006.12:30153833:C= (self)
ss76898269 NT_007592.14:20979861:C= NC_000006.12:30153833:C= (self)
ss84529029 NC_000006.9:30229589:C>T NC_000006.12:30153833:C>T (self)
ss201597488, ss485225754, ss1592291755 NC_000006.10:30229589:C>T NC_000006.12:30153833:C>T (self)
31277546, 17437377, 12426193, 177940528, 17437377, ss222292003, ss240458878, ss484132853, ss536322774, ss653018911, ss779440521, ss782511986, ss834909963, ss982744395, ss1319512138, ss1581596259, ss1584044750, ss1615250949, ss1658244982, ss1711118832, ss1925996572, ss1970350400, ss2023626664, ss2151791946, ss2451242247, ss2634424406, ss2837312771, ss2998765508, ss3629492406, ss3632343605, ss3646333140 NC_000006.11:30121610:C>T NC_000006.12:30153833:C>T (self)
334861882, ss2282872328, ss3493598238 NC_000006.12:30153833:C>T NC_000006.12:30153833:C>T (self)
ss76898269 NT_007592.14:20979861:C>T NC_000006.12:30153833: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 rs55670497

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.post58+e54ea20