Skip to main page content
Accesskeys

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.

rs145172824

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr6:30156968 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.00005 (13/241042, GnomAD)
A=0.00007 (9/125568, TOPMED)
A=0.00005 (6/116058, ExAC) (+ 3 more)
A=0.0001 (2/30980, GnomAD)
A=0.000 (1/8432, GO-ESP)
A=0.000 (1/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TRIM10 : 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.p12 chr 6 NC_000006.12:g.30156968G>A
GRCh37.p13 chr 6 NC_000006.11:g.30124745G>A
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.1636776G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.1636882G>A
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.1412097G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.1417693G>A
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.1412885G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.1418470G>A
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.1455896G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.1455194G>A
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.1467690G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.1473310G>A
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.1501046G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.1506631G>A
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.2:g.1415064G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.1:g.1364980G>A
Gene: TRIM10, tripartite motif containing 10 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TRIM10 transcript variant 2 NM_052828.2:c.866C>T P [CCG] > L [CTG] Coding Sequence Variant
tripartite motif-containing protein 10 isoform 2 NP_439893.2:p.Pro289Leu P (Pro) > L (Leu) Missense Variant
TRIM10 transcript variant 1 NM_006778.3:c.866C>T P [CCG] > L [CTG] Coding Sequence Variant
tripartite motif-containing protein 10 isoform 1 NP_006769.2:p.Pro289Leu P (Pro) > L (Leu) Missense Variant
TRIM10 transcript variant X1 XM_011514221.1:c.920C>T P [CCG] > L [CTG] Coding Sequence Variant
tripartite motif-containing protein 10 isoform X1 XP_011512523.1:p.Pro307Leu P (Pro) > L (Leu) Missense Variant
TRIM10 transcript variant X4 XM_011514225.1:c.920C>T P [CCG] > L [CTG] Coding Sequence Variant
tripartite motif-containing protein 10 isoform X2 XP_011512527.1:p.Pro307Leu P (Pro) > L (Leu) Missense Variant
TRIM10 transcript variant X2 XM_011514222.2:c.920C>T P [CCG] > L [CTG] Coding Sequence Variant
tripartite motif-containing protein 10 isoform X1 XP_011512524.1:p.Pro307Leu P (Pro) > L (Leu) Missense Variant
TRIM10 transcript variant X3 XM_011514223.2:c.920C>T P [CCG] > L [CTG] Coding Sequence Variant
tripartite motif-containing protein 10 isoform X1 XP_011512525.1:p.Pro307Leu P (Pro) > L (Leu) Missense 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
gnomAD - Exomes Global Study-wide 241042 G=0.99995 A=0.00005
gnomAD - Exomes European Sub 130574 G=0.99996 A=0.00004
gnomAD - Exomes Asian Sub 47682 G=1.0000 A=0.0000
gnomAD - Exomes American Sub 33470 G=0.9998 A=0.0002
gnomAD - Exomes African Sub 14188 G=0.9999 A=0.0001
gnomAD - Exomes Ashkenazi Jewish Sub 9720 G=1.000 A=0.000
gnomAD - Exomes Other Sub 5408 G=1.000 A=0.000
TopMed Global Study-wide 125568 G=0.99993 A=0.00007
ExAC Global Study-wide 116058 G=0.99995 A=0.00005
ExAC Europe Sub 69868 G=0.9999 A=0.0001
ExAC Asian Sub 24710 G=1.0000 A=0.0000
ExAC American Sub 11454 G=0.9999 A=0.0001
ExAC African Sub 9154 G=1.000 A=0.000
ExAC Other Sub 872 G=1.00 A=0.00
gnomAD - Genomes Global Study-wide 30980 G=0.9999 A=0.0001
gnomAD - Genomes European Sub 18504 G=1.0000 A=0.0000
gnomAD - Genomes African Sub 8732 G=1.000 A=0.000
gnomAD - Genomes East Asian Sub 1622 G=1.000 A=0.000
gnomAD - Genomes Other Sub 982 G=1.00 A=0.00
gnomAD - Genomes American Sub 838 G=1.00 A=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 302 G=1.00 A=0.00
GO Exome Sequencing Project Global Study-wide 8432 G=1.000 A=0.000
GO Exome Sequencing Project European American Sub 5416 G=1.000 A=0.000
GO Exome Sequencing Project African American Sub 3016 G=1.000 A=0.000
1000Genomes Global Study-wide 5008 G=1.000 A=0.000
1000Genomes African Sub 1322 G=1.000 A=0.000
1000Genomes East Asian Sub 1008 G=0.999 A=0.001
1000Genomes Europe Sub 1006 G=1.000 A=0.000
1000Genomes South Asian Sub 978 G=1.00 A=0.00
1000Genomes American Sub 694 G=1.00 A=0.00
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 Note
GRCh38.p12 chr 6 NC_000006.12:g.30156968G= NC_000006.12:g.30156968G>A
GRCh37.p13 chr 6 NC_000006.11:g.30124745G= NC_000006.11:g.30124745G>A
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.1636776G= NT_113891.3:g.1636776G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.1636882G= NT_113891.2:g.1636882G>A
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.1412097G= NT_167248.2:g.1412097G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.1417693G= NT_167248.1:g.1417693G>A
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.1412885G= NT_167245.2:g.1412885G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.1418470G= NT_167245.1:g.1418470G>A
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.1455896G= NT_167249.2:g.1455896G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.1455194G= NT_167249.1:g.1455194G>A
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.1467690G= NT_167246.2:g.1467690G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.1473310G= NT_167246.1:g.1473310G>A
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.1501046G= NT_167247.2:g.1501046G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.1506631G= NT_167247.1:g.1506631G>A
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.2:g.1415064G= NT_167244.2:g.1415064G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.1:g.1364980G= NT_167244.1:g.1364980G>A
TRIM10 transcript variant 1 NM_006778.3:c.866C= NM_006778.3:c.866C>T
TRIM10 transcript variant 2 NM_052828.2:c.866C= NM_052828.2:c.866C>T
TRIM10 transcript variant X3 XM_011514223.2:c.920C= XM_011514223.2:c.920C>T
TRIM10 transcript variant X2 XM_011514222.2:c.920C= XM_011514222.2:c.920C>T
TRIM10 transcript variant X4 XM_011514225.1:c.920C= XM_011514225.1:c.920C>T
TRIM10 transcript variant X1 XM_011514221.1:c.920C= XM_011514221.1:c.920C>T
tripartite motif-containing protein 10 isoform 1 NP_006769.2:p.Pro289= NP_006769.2:p.Pro289Leu
tripartite motif-containing protein 10 isoform 2 NP_439893.2:p.Pro289= NP_439893.2:p.Pro289Leu
tripartite motif-containing protein 10 isoform X1 XP_011512525.1:p.Pro307= XP_011512525.1:p.Pro307Leu
tripartite motif-containing protein 10 isoform X1 XP_011512524.1:p.Pro307= XP_011512524.1:p.Pro307Leu
tripartite motif-containing protein 10 isoform X2 XP_011512527.1:p.Pro307= XP_011512527.1:p.Pro307Leu
tripartite motif-containing protein 10 isoform X1 XP_011512523.1:p.Pro307= XP_011512523.1:p.Pro307Leu
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#.

10 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342205204 May 09, 2011 (134)
2 1000GENOMES ss1319512249 Aug 21, 2014 (142)
3 EVA_DECODE ss1592291792 Apr 01, 2015 (144)
4 EVA_EXAC ss1688213989 Apr 01, 2015 (144)
5 HUMAN_LONGEVITY ss2282872513 Dec 20, 2016 (150)
6 TOPMED ss2451242434 Dec 20, 2016 (150)
7 GNOMAD ss2735622200 Nov 08, 2017 (151)
8 GNOMAD ss2747573022 Nov 08, 2017 (151)
9 GNOMAD ss2837313026 Nov 08, 2017 (151)
10 TOPMED ss3493598771 Nov 08, 2017 (151)
11 1000Genomes NC_000006.11 - 30124745 Oct 12, 2018 (152)
12 ExAC NC_000006.11 - 30124745 Oct 12, 2018 (152)
13 gnomAD - Genomes NC_000006.11 - 30124745 Oct 12, 2018 (152)
14 gnomAD - Exomes NC_000006.11 - 30124745 Oct 12, 2018 (152)
15 GO Exome Sequencing Project NC_000006.11 - 30124745 Oct 12, 2018 (152)
16 TopMed NC_000006.12 - 30156968 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
ss1592291792 NC_000006.10:30232723:G= NC_000006.12:30156967:G= (self)
31277661, 8237677, 177940783, 3794452, 625095, ss342205204, ss1319512249, ss1688213989, ss2451242434, ss2735622200, ss2747573022, ss2837313026 NC_000006.11:30124744:G= NC_000006.12:30156967:G= (self)
334862359, ss2282872513, ss3493598771 NC_000006.12:30156967:G= NC_000006.12:30156967:G= (self)
ss1592291792 NC_000006.10:30232723:G>A NC_000006.12:30156967:G>A (self)
31277661, 8237677, 177940783, 3794452, 625095, ss342205204, ss1319512249, ss1688213989, ss2451242434, ss2735622200, ss2747573022, ss2837313026 NC_000006.11:30124744:G>A NC_000006.12:30156967:G>A (self)
334862359, ss2282872513, ss3493598771 NC_000006.12:30156967:G>A NC_000006.12:30156967: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 rs145172824

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