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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 Aliases 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.

rs117744954

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr6:30344182 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.00032 (40/125568, TOPMED)
C=0.0001 (2/31390, GnomAD)
C=0.008 (39/5008, 1000G) (+ 2 more)
C=0.000 (1/3854, ALSPAC)
C=0.000 (0/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TRIM39-RPP21 : Intron Variant
RPP21 : 2KB Upstream Variant
TRIM39 : 500B Downstream 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.30344182T>C
GRCh37.p13 chr 6 NC_000006.11:g.30311959T>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.1823863T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.1823969T>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.1599264T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.1604860T>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.1600028T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.1605613T>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.1642639T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.1641937T>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.1654414T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.1660034T>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.2:g.1673678T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.1:g.1623594T>C
Gene: TRIM39-RPP21, TRIM39-RPP21 readthrough (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TRIM39-RPP21 transcript NM_001199119.1:c. N/A Intron Variant
Gene: RPP21, ribonuclease P/MRP subunit p21 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
RPP21 transcript variant 1 NM_001199120.2:c. N/A Upstream Transcript Variant
RPP21 transcript variant 3 NM_001199121.2:c. N/A Upstream Transcript Variant
RPP21 transcript variant 2 NM_024839.3:c. N/A Upstream Transcript Variant
Gene: TRIM39, tripartite motif containing 39 (plus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
TRIM39 transcript variant 3 NM_001369521.1:c. N/A Downstream Transcript Variant
TRIM39 transcript variant 4 NM_001369522.1:c. N/A Downstream Transcript Variant
TRIM39 transcript variant 5 NM_001369523.1:c. N/A Downstream Transcript Variant
TRIM39 transcript variant 1 NM_021253.4:c. N/A Downstream Transcript Variant
TRIM39 transcript variant 2 NM_172016.2:c. N/A 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
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 T=0.99968 C=0.00032
gnomAD - Genomes Global Study-wide 31390 T=0.9999 C=0.0001
gnomAD - Genomes European Sub 18902 T=1.0000 C=0.0000
gnomAD - Genomes African Sub 8704 T=1.000 C=0.000
gnomAD - Genomes East Asian Sub 1560 T=1.000 C=0.000
gnomAD - Genomes Other Sub 1086 T=0.998 C=0.002
gnomAD - Genomes American Sub 848 T=1.00 C=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=1.00 C=0.00
1000Genomes Global Study-wide 5008 T=0.992 C=0.008
1000Genomes African Sub 1322 T=1.000 C=0.000
1000Genomes East Asian Sub 1008 T=0.977 C=0.023
1000Genomes Europe Sub 1006 T=1.000 C=0.000
1000Genomes South Asian Sub 978 T=0.98 C=0.02
1000Genomes American Sub 694 T=1.00 C=0.00
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=1.000 C=0.000
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=1.000 C=0.000
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 Note
GRCh38.p12 chr 6 NC_000006.12:g.30344182= NC_000006.12:g.30344182T>C
GRCh37.p13 chr 6 NC_000006.11:g.30311959= NC_000006.11:g.30311959T>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.1823863= NT_113891.3:g.1823863T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.1823969= NT_113891.2:g.1823969T>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.1599264= NT_167248.2:g.1599264T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.1604860= NT_167248.1:g.1604860T>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.1600028= NT_167245.2:g.1600028T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.1605613= NT_167245.1:g.1605613T>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.1642639= NT_167249.2:g.1642639T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.1641937= NT_167249.1:g.1641937T>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.1654414= NT_167246.2:g.1654414T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.1660034= NT_167246.1:g.1660034T>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.2:g.1673678= NT_167244.2:g.1673678T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.1:g.1623594= NT_167244.1:g.1623594T>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#.

13 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss240459482 Jul 15, 2010 (132)
2 ILLUMINA ss534213489 Sep 08, 2015 (146)
3 EVA-GONL ss982746217 Aug 21, 2014 (142)
4 1000GENOMES ss1319517127 Aug 21, 2014 (142)
5 EVA_UK10K_ALSPAC ss1615254084 Apr 01, 2015 (144)
6 EVA_UK10K_TWINSUK ss1658248117 Apr 01, 2015 (144)
7 HUMAN_LONGEVITY ss2282881952 Dec 20, 2016 (150)
8 TOPMED ss2451251950 Dec 20, 2016 (150)
9 GRF ss2707385175 Nov 08, 2017 (151)
10 GNOMAD ss2837326330 Nov 08, 2017 (151)
11 TOPMED ss3493627901 Nov 08, 2017 (151)
12 ILLUMINA ss3629493556 Oct 12, 2018 (152)
13 EVA ss3764801084 Jul 13, 2019 (153)
14 1000Genomes NC_000006.11 - 30311959 Oct 12, 2018 (152)
15 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 30311959 Oct 12, 2018 (152)
16 gnomAD - Genomes NC_000006.11 - 30311959 Jul 13, 2019 (153)
17 TopMed NC_000006.12 - 30344182 Oct 12, 2018 (152)
18 UK 10K study - Twins NC_000006.11 - 30311959 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
31282763, 17440875, 85575254, 17440875, ss240459482, ss534213489, ss982746217, ss1319517127, ss1615254084, ss1658248117, ss2451251950, ss2707385175, ss2837326330, ss3629493556, ss3764801084 NC_000006.11:30311958:T:C NC_000006.12:30344181:T:C (self)
334886029, ss2282881952, ss3493627901 NC_000006.12:30344181:T:C NC_000006.12:30344181: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 rs117744954

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.post308+0fe9b3b