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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.

rs758629425

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:31170423 (GRCh38.p14) 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=0.000068 (18/264690, TOPMED)
T=0.000025 (6/243686, GnomAD_exome)
T=0.000036 (5/140262, GnomAD) (+ 2 more)
T=0.000030 (3/100800, ExAC)
T=0.00009 (2/23038, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
POU5F1 : Synonymous Variant
Publications
0 citations
Genomic View
See rs on genome

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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 23038 C=0.99991 T=0.00009
European Sub 15752 C=0.99994 T=0.00006
African Sub 3492 C=0.9997 T=0.0003
African Others Sub 122 C=1.000 T=0.000
African American Sub 3370 C=0.9997 T=0.0003
Asian Sub 168 C=1.000 T=0.000
East Asian Sub 112 C=1.000 T=0.000
Other Asian Sub 56 C=1.00 T=0.00
Latin American 1 Sub 146 C=1.000 T=0.000
Latin American 2 Sub 610 C=1.000 T=0.000
South Asian Sub 98 C=1.00 T=0.00
Other Sub 2772 C=1.0000 T=0.0000


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 C=0.999932 T=0.000068
gnomAD - Exomes Global Study-wide 243686 C=0.999975 T=0.000025
gnomAD - Exomes European Sub 130338 C=0.999985 T=0.000015
gnomAD - Exomes Asian Sub 48490 C=0.99998 T=0.00002
gnomAD - Exomes American Sub 34340 C=1.00000 T=0.00000
gnomAD - Exomes African Sub 14630 C=0.99979 T=0.00021
gnomAD - Exomes Ashkenazi Jewish Sub 9902 C=1.0000 T=0.0000
gnomAD - Exomes Other Sub 5986 C=1.0000 T=0.0000
gnomAD - Genomes Global Study-wide 140262 C=0.999964 T=0.000036
gnomAD - Genomes European Sub 75930 C=0.99999 T=0.00001
gnomAD - Genomes African Sub 42058 C=0.99990 T=0.00010
gnomAD - Genomes American Sub 13670 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3128 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2154 C=1.0000 T=0.0000
ExAC Global Study-wide 100800 C=0.999970 T=0.000030
ExAC Europe Sub 60140 C=1.00000 T=0.00000
ExAC Asian Sub 22318 C=1.00000 T=0.00000
ExAC American Sub 10206 C=1.00000 T=0.00000
ExAC African Sub 7404 C=0.9997 T=0.0003
ExAC Other Sub 732 C=0.999 T=0.001
Allele Frequency Aggregator Total Global 23038 C=0.99991 T=0.00009
Allele Frequency Aggregator European Sub 15752 C=0.99994 T=0.00006
Allele Frequency Aggregator African Sub 3492 C=0.9997 T=0.0003
Allele Frequency Aggregator Other Sub 2772 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 168 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
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.p14 chr 6 NC_000006.12:g.31170423C>T
GRCh37.p13 chr 6 NC_000006.11:g.31138200C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.2652865C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.2652971C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.2428473C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.2434069C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.2429757C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.2435342C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.2473855C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.2473153C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.2480943C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.2486563C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.2514557C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.2520142C>T
Gene: POU5F1, POU class 5 homeobox 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
POU5F1 transcript variant 3 NM_001173531.3:c. N/A Genic Upstream Transcript Variant
POU5F1 transcript variant 4 NM_001285986.2:c. N/A Genic Upstream Transcript Variant
POU5F1 transcript variant 2 NM_203289.6:c. N/A Genic Upstream Transcript Variant
POU5F1 transcript variant 1 NM_002701.6:c.198G>A P [CCG] > P [CCA] Coding Sequence Variant
POU domain, class 5, transcription factor 1 isoform 1 NP_002692.2:p.Pro66= P (Pro) > P (Pro) Synonymous 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

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
GRCh38.p14 chr 6 NC_000006.12:g.31170423= NC_000006.12:g.31170423C>T
GRCh37.p13 chr 6 NC_000006.11:g.31138200= NC_000006.11:g.31138200C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.2652865= NT_113891.3:g.2652865C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.2652971= NT_113891.2:g.2652971C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.2428473= NT_167248.2:g.2428473C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.2434069= NT_167248.1:g.2434069C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.2429757= NT_167245.2:g.2429757C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.2435342= NT_167245.1:g.2435342C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.2473855= NT_167249.2:g.2473855C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.2473153= NT_167249.1:g.2473153C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.2480943= NT_167246.2:g.2480943C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.2486563= NT_167246.1:g.2486563C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.2514557= NT_167247.2:g.2514557C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.2520142= NT_167247.1:g.2520142C>T
POU5F1 transcript variant 1 NM_002701.6:c.198= NM_002701.6:c.198G>A
POU5F1 transcript variant 1 NM_002701.5:c.198= NM_002701.5:c.198G>A
POU5F1 transcript variant 1 NM_002701.4:c.198= NM_002701.4:c.198G>A
POU domain, class 5, transcription factor 1 isoform 1 NP_002692.2:p.Pro66= NP_002692.2:p.Pro66=
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#.

6 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1688227359 Apr 01, 2015 (144)
2 GNOMAD ss2735644087 Nov 08, 2017 (151)
3 GNOMAD ss2747580024 Nov 08, 2017 (151)
4 GNOMAD ss2837390677 Nov 08, 2017 (151)
5 TOPMED ss4698316507 Apr 26, 2021 (155)
6 EVA ss5364703347 Oct 17, 2022 (156)
7 ExAC NC_000006.11 - 31138200 Oct 12, 2018 (152)
8 gnomAD - Genomes NC_000006.12 - 31170423 Apr 26, 2021 (155)
9 gnomAD - Exomes NC_000006.11 - 31138200 Jul 13, 2019 (153)
10 TopMed NC_000006.12 - 31170423 Apr 26, 2021 (155)
11 ALFA NC_000006.12 - 31170423 Apr 26, 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
8252202, 4786836, ss1688227359, ss2735644087, ss2747580024, ss2837390677, ss5364703347 NC_000006.11:31138199:C:T NC_000006.12:31170422:C:T (self)
221140721, 535694065, 12448826334, ss4698316507 NC_000006.12:31170422:C:T NC_000006.12:31170422: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 rs758629425

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.post761+d5e8e07