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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.

rs375009107

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr13:27920422 (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>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000053 (14/264690, TOPMED)
A=0.000087 (15/172498, GnomAD_exome)
A=0.000057 (8/140282, GnomAD) (+ 3 more)
A=0.00016 (7/44394, ALFA)
A=0.00043 (8/18396, ExAC)
A=0.00009 (1/11666, GO-ESP)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PDX1 : Missense 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 44394 C=0.99984 A=0.00016
European Sub 32624 C=0.99985 A=0.00015
African Sub 3512 C=1.0000 A=0.0000
African Others Sub 122 C=1.000 A=0.000
African American Sub 3390 C=1.0000 A=0.0000
Asian Sub 168 C=1.000 A=0.000
East Asian Sub 112 C=1.000 A=0.000
Other Asian Sub 56 C=1.00 A=0.00
Latin American 1 Sub 500 C=1.000 A=0.000
Latin American 2 Sub 628 C=1.000 A=0.000
South Asian Sub 98 C=1.00 A=0.00
Other Sub 6864 C=0.9997 A=0.0003


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=0.999947 A=0.000053
gnomAD - Exomes Global Study-wide 172498 C=0.999913 A=0.000087
gnomAD - Exomes European Sub 86138 C=0.99985 A=0.00015
gnomAD - Exomes Asian Sub 37554 C=1.00000 A=0.00000
gnomAD - Exomes American Sub 26742 C=0.99993 A=0.00007
gnomAD - Exomes African Sub 8856 C=1.0000 A=0.0000
gnomAD - Exomes Ashkenazi Jewish Sub 8566 C=1.0000 A=0.0000
gnomAD - Exomes Other Sub 4642 C=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 140282 C=0.999943 A=0.000057
gnomAD - Genomes European Sub 75952 C=0.99991 A=0.00009
gnomAD - Genomes African Sub 42052 C=0.99998 A=0.00002
gnomAD - Genomes American Sub 13666 C=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 C=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2154 C=1.0000 A=0.0000
Allele Frequency Aggregator Total Global 44394 C=0.99984 A=0.00016
Allele Frequency Aggregator European Sub 32624 C=0.99985 A=0.00015
Allele Frequency Aggregator Other Sub 6864 C=0.9997 A=0.0003
Allele Frequency Aggregator African Sub 3512 C=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 628 C=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 C=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 168 C=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 A=0.00
ExAC Global Study-wide 18396 C=0.99957 A=0.00043
ExAC Asian Sub 9010 C=1.0000 A=0.0000
ExAC Europe Sub 7408 C=0.9989 A=0.0011
ExAC African Sub 1228 C=1.0000 A=0.0000
ExAC American Sub 568 C=1.000 A=0.000
ExAC Other Sub 182 C=1.000 A=0.000
GO Exome Sequencing Project Global Study-wide 11666 C=0.99991 A=0.00009
GO Exome Sequencing Project European American Sub 7752 C=0.9999 A=0.0001
GO Exome Sequencing Project African American Sub 3914 C=1.0000 A=0.0000
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 13 NC_000013.11:g.27920422C>A
GRCh37.p13 chr 13 NC_000013.10:g.28494559C>A
PDX1 RefSeqGene NG_008183.1:g.5392C>A
Gene: PDX1, pancreatic and duodenal homeobox 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PDX1 transcript NM_000209.4:c.284C>A P [CCG] > Q [CAG] Coding Sequence Variant
pancreas/duodenum homeobox protein 1 NP_000200.1:p.Pro95Gln P (Pro) > Q (Gln) 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

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= A
GRCh38.p14 chr 13 NC_000013.11:g.27920422= NC_000013.11:g.27920422C>A
GRCh37.p13 chr 13 NC_000013.10:g.28494559= NC_000013.10:g.28494559C>A
PDX1 RefSeqGene NG_008183.1:g.5392= NG_008183.1:g.5392C>A
PDX1 transcript NM_000209.4:c.284= NM_000209.4:c.284C>A
PDX1 transcript NM_000209.3:c.284= NM_000209.3:c.284C>A
pancreas/duodenum homeobox protein 1 NP_000200.1:p.Pro95= NP_000200.1:p.Pro95Gln
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 ss713143425 Apr 25, 2013 (138)
2 EVA_EXAC ss1691238504 Apr 01, 2015 (144)
3 HUMAN_LONGEVITY ss2195060907 Dec 20, 2016 (150)
4 GNOMAD ss2749023909 Nov 08, 2017 (151)
5 GNOMAD ss2917887185 Nov 08, 2017 (151)
6 ILLUMINA ss3021493924 Nov 08, 2017 (151)
7 ILLUMINA ss3651879200 Oct 12, 2018 (152)
8 EVA ss3824798947 Apr 27, 2020 (154)
9 EVA ss3825834561 Apr 27, 2020 (154)
10 TOPMED ss4940824769 Apr 26, 2021 (155)
11 ExAC NC_000013.10 - 28494559 Oct 12, 2018 (152)
12 gnomAD - Genomes NC_000013.11 - 27920422 Apr 26, 2021 (155)
13 gnomAD - Exomes NC_000013.10 - 28494559 Jul 13, 2019 (153)
14 GO Exome Sequencing Project NC_000013.10 - 28494559 Oct 12, 2018 (152)
15 TopMed NC_000013.11 - 27920422 Apr 26, 2021 (155)
16 ALFA NC_000013.11 - 27920422 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
1563198, 9576379, 1256335, ss713143425, ss1691238504, ss2749023909, ss2917887185, ss3021493924, ss3651879200, ss3824798947, ss3825834561 NC_000013.10:28494558:C:A NC_000013.11:27920421:C:A (self)
426237755, 156370427, 324938101, ss2195060907, ss4940824769 NC_000013.11:27920421:C:A NC_000013.11:27920421:C: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 rs375009107

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