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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.

rs375623969

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr17:72124405 (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
G>A / G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000026 (7/264690, TOPMED)
A=0.000043 (6/140266, GnomAD)
A=0.00007 (1/14050, ALFA) (+ 1 more)
T=0.00008 (1/13004, GO-ESP)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SOX9 : 3 Prime UTR 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 14050 G=0.99993 A=0.00007
European Sub 9690 G=1.0000 A=0.0000
African Sub 2898 G=1.0000 A=0.0000
African Others Sub 114 G=1.000 A=0.000
African American Sub 2784 G=1.0000 A=0.0000
Asian Sub 112 G=1.000 A=0.000
East Asian Sub 86 G=1.00 A=0.00
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 146 G=1.000 A=0.000
Latin American 2 Sub 610 G=1.000 A=0.000
South Asian Sub 98 G=0.99 A=0.01
Other Sub 496 G=1.000 A=0.000


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 G=0.999974 A=0.000026
gnomAD - Genomes Global Study-wide 140266 G=0.999957 A=0.000043
gnomAD - Genomes European Sub 75954 G=0.99995 A=0.00005
gnomAD - Genomes African Sub 42042 G=1.00000 A=0.00000
gnomAD - Genomes American Sub 13668 G=0.99985 A=0.00015
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3130 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2150 G=1.0000 A=0.0000
Allele Frequency Aggregator Total Global 14050 G=0.99993 A=0.00007
Allele Frequency Aggregator European Sub 9690 G=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 2898 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000
Allele Frequency Aggregator Other Sub 496 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 112 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=0.99 A=0.01
GO Exome Sequencing Project Global Study-wide 13004 G=0.99992 T=0.00008
GO Exome Sequencing Project European American Sub 8598 G=0.9999 T=0.0001
GO Exome Sequencing Project African American Sub 4406 G=1.0000 T=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 17 NC_000017.11:g.72124405G>A
GRCh38.p14 chr 17 NC_000017.11:g.72124405G>C
GRCh38.p14 chr 17 NC_000017.11:g.72124405G>T
GRCh37.p13 chr 17 NC_000017.10:g.70120546G>A
GRCh37.p13 chr 17 NC_000017.10:g.70120546G>C
GRCh37.p13 chr 17 NC_000017.10:g.70120546G>T
SOX9 RefSeqGene NG_012490.1:g.8386G>A
SOX9 RefSeqGene NG_012490.1:g.8386G>C
SOX9 RefSeqGene NG_012490.1:g.8386G>T
Gene: SOX9, SRY-box transcription factor 9 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SOX9 transcript NM_000346.4:c.*18= 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

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 C T
GRCh38.p14 chr 17 NC_000017.11:g.72124405= NC_000017.11:g.72124405G>A NC_000017.11:g.72124405G>C NC_000017.11:g.72124405G>T
GRCh37.p13 chr 17 NC_000017.10:g.70120546= NC_000017.10:g.70120546G>A NC_000017.10:g.70120546G>C NC_000017.10:g.70120546G>T
SOX9 RefSeqGene NG_012490.1:g.8386= NG_012490.1:g.8386G>A NG_012490.1:g.8386G>C NG_012490.1:g.8386G>T
SOX9 transcript NM_000346.4:c.*18= NM_000346.4:c.*18G>A NM_000346.4:c.*18G>C NM_000346.4:c.*18G>T
SOX9 transcript NM_000346.3:c.*18= NM_000346.3:c.*18G>A NM_000346.3:c.*18G>C NM_000346.3:c.*18G>T
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#.

11 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss713407630 Apr 25, 2013 (138)
2 EVA_EXAC ss1692941442 Apr 01, 2015 (144)
3 EVA_EXAC ss1692941443 Apr 01, 2015 (144)
4 HUMAN_LONGEVITY ss2218429597 Dec 20, 2016 (150)
5 GNOMAD ss2742970504 Nov 08, 2017 (151)
6 GNOMAD ss2749851017 Nov 08, 2017 (151)
7 GNOMAD ss2952202748 Nov 08, 2017 (151)
8 EVA ss3825147383 Apr 27, 2020 (154)
9 TOPMED ss5043061195 Apr 26, 2021 (155)
10 EVA ss5936351911 Oct 16, 2022 (156)
11 EVA ss5936351912 Oct 16, 2022 (156)
12 ExAC

Submission ignored due to conflicting rows:
Row 3397440 (NC_000017.10:70120545:G:G 117414/117426, NC_000017.10:70120545:G:A 12/117426)
Row 3397441 (NC_000017.10:70120545:G:G 117425/117426, NC_000017.10:70120545:G:T 1/117426)

- Oct 12, 2018 (152)
13 ExAC

Submission ignored due to conflicting rows:
Row 3397440 (NC_000017.10:70120545:G:G 117414/117426, NC_000017.10:70120545:G:A 12/117426)
Row 3397441 (NC_000017.10:70120545:G:G 117425/117426, NC_000017.10:70120545:G:T 1/117426)

- Oct 12, 2018 (152)
14 gnomAD - Genomes NC_000017.11 - 72124405 Apr 26, 2021 (155)
15 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 12278165 (NC_000017.10:70120545:G:G 237969/237996, NC_000017.10:70120545:G:A 27/237996)
Row 12278166 (NC_000017.10:70120545:G:G 237995/237996, NC_000017.10:70120545:G:T 1/237996)

- Jul 13, 2019 (153)
16 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 12278165 (NC_000017.10:70120545:G:G 237969/237996, NC_000017.10:70120545:G:A 27/237996)
Row 12278166 (NC_000017.10:70120545:G:G 237995/237996, NC_000017.10:70120545:G:T 1/237996)

- Jul 13, 2019 (153)
17 GO Exome Sequencing Project NC_000017.10 - 70120546 Oct 12, 2018 (152)
18 TopMed NC_000017.11 - 72124405 Apr 26, 2021 (155)
19 ALFA NC_000017.11 - 72124405 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
ss1692941442, ss2742970504, ss2749851017, ss2952202748, ss5936351911, ss5936351912 NC_000017.10:70120545:G:A NC_000017.11:72124404:G:A (self)
513212284, 258606857, 1618397841, ss2218429597, ss5043061195 NC_000017.11:72124404:G:A NC_000017.11:72124404:G:A (self)
ss5936351911, ss5936351912 NC_000017.10:70120545:G:C NC_000017.11:72124404:G:C
1604444, ss713407630, ss1692941443, ss2742970504, ss3825147383, ss5936351911, ss5936351912 NC_000017.10:70120545:G:T NC_000017.11:72124404:G: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 rs375623969

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