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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs1489191203

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr7:18793393 (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=0.000008 (2/264690, TOPMED)
T=0.000007 (1/140232, GnomAD)
T=0.00003 (1/35422, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HDAC9 : 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 35422 C=0.99997 T=0.00003 0.999944 0.0 5.6e-05 0
European Sub 26580 C=0.99996 T=0.00004 0.999925 0.0 0.000075 0
African Sub 2918 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 C=1.000 T=0.000 1.0 0.0 0.0 N/A
African American Sub 2804 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 C=1.000 T=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 500 C=1.000 T=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 628 C=1.000 T=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Sub 4586 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A


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=0.999992 T=0.000008
gnomAD - Genomes Global Study-wide 140232 C=0.999993 T=0.000007
gnomAD - Genomes European Sub 75954 C=0.99999 T=0.00001
gnomAD - Genomes African Sub 42018 C=1.00000 T=0.00000
gnomAD - Genomes American Sub 13650 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3132 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2154 C=1.0000 T=0.0000
Allele Frequency Aggregator Total Global 35422 C=0.99997 T=0.00003
Allele Frequency Aggregator European Sub 26580 C=0.99996 T=0.00004
Allele Frequency Aggregator Other Sub 4586 C=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 2918 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 628 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 112 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 7 NC_000007.14:g.18793393C>T
GRCh37.p13 chr 7 NC_000007.13:g.18833016C>T
HDAC9 RefSeqGene NG_023250.3:g.711445C>T
Gene: HDAC9, histone deacetylase 9 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
HDAC9 transcript variant 6 NM_001204144.3:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 7 NM_001204145.3:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 8 NM_001204146.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 9 NM_001204147.3:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 10 NM_001204148.3:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 12 NM_001321869.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 13 NM_001321870.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 14 NM_001321871.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 15 NM_001321872.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 16 NM_001321873.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 17 NM_001321874.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 18 NM_001321875.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 19 NM_001321876.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 21 NM_001321878.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 22 NM_001321879.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 23 NM_001321884.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 24 NM_001321885.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 25 NM_001321886.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 26 NM_001321887.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 27 NM_001321888.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 28 NM_001321889.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 29 NM_001321890.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 30 NM_001321891.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 31 NM_001321893.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 32 NM_001321894.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 33 NM_001321895.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 34 NM_001321896.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 36 NM_001321898.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 37 NM_001321899.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 38 NM_001321900.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 39 NM_001321901.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 40 NM_001321902.2:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 3 NM_014707.4:c. N/A Genic Downstream Transcript Variant
HDAC9 transcript variant 1 NM_058176.2:c.2254C>T R [CGC] > C [TGC] Coding Sequence Variant
histone deacetylase 9 isoform 1 NP_478056.1:p.Arg752Cys R (Arg) > C (Cys) Missense Variant
HDAC9 transcript variant 35 NM_001321897.2:c.2131C>T R [CGC] > C [TGC] Coding Sequence Variant
histone deacetylase 9 isoform 20 NP_001308826.1:p.Arg711Cys R (Arg) > C (Cys) Missense Variant
HDAC9 transcript variant 11 NM_001321868.2:c.2188C>T R [CGC] > C [TGC] Coding Sequence Variant
histone deacetylase 9 isoform 11 NP_001308797.1:p.Arg730Cys R (Arg) > C (Cys) Missense Variant
HDAC9 transcript variant 4 NM_178423.3:c.2254C>T R [CGC] > C [TGC] Coding Sequence Variant
histone deacetylase 9 isoform 4 NP_848510.1:p.Arg752Cys R (Arg) > C (Cys) Missense Variant
HDAC9 transcript variant 20 NM_001321877.2:c.2131C>T R [CGC] > C [TGC] Coding Sequence Variant
histone deacetylase 9 isoform 20 NP_001308806.1:p.Arg711Cys R (Arg) > C (Cys) Missense Variant
HDAC9 transcript variant 5 NM_178425.4:c.2263C>T R [CGC] > C [TGC] Coding Sequence Variant
histone deacetylase 9 isoform 5 NP_848512.1:p.Arg755Cys R (Arg) > C (Cys) Missense Variant
HDAC9 transcript variant 41 NR_135835.2:n. N/A Genic 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

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 7 NC_000007.14:g.18793393= NC_000007.14:g.18793393C>T
GRCh37.p13 chr 7 NC_000007.13:g.18833016= NC_000007.13:g.18833016C>T
HDAC9 RefSeqGene NG_023250.3:g.711445= NG_023250.3:g.711445C>T
HDAC9 transcript variant 5 NM_178425.4:c.2263= NM_178425.4:c.2263C>T
HDAC9 transcript variant 5 NM_178425.3:c.2263= NM_178425.3:c.2263C>T
HDAC9 transcript variant 5 NM_178425.2:c.2263= NM_178425.2:c.2263C>T
HDAC9 transcript variant 4 NM_178423.3:c.2254= NM_178423.3:c.2254C>T
HDAC9 transcript variant 4 NM_178423.2:c.2254= NM_178423.2:c.2254C>T
HDAC9 transcript variant 4 NM_178423.1:c.2254= NM_178423.1:c.2254C>T
HDAC9 transcript variant 11 NM_001321868.2:c.2188= NM_001321868.2:c.2188C>T
HDAC9 transcript variant 11 NM_001321868.1:c.2188= NM_001321868.1:c.2188C>T
HDAC9 transcript variant 20 NM_001321877.2:c.2131= NM_001321877.2:c.2131C>T
HDAC9 transcript variant 20 NM_001321877.1:c.2131= NM_001321877.1:c.2131C>T
HDAC9 transcript variant 35 NM_001321897.2:c.2131= NM_001321897.2:c.2131C>T
HDAC9 transcript variant 35 NM_001321897.1:c.2131= NM_001321897.1:c.2131C>T
HDAC9 transcript variant 1 NM_058176.2:c.2254= NM_058176.2:c.2254C>T
HDAC9 transcript variant 2 NM_058177.2:c.2254= NM_058177.2:c.2254C>T
HDAC9 transcript variant 2 NM_058177.1:c.2254= NM_058177.1:c.2254C>T
histone deacetylase 9 isoform 5 NP_848512.1:p.Arg755= NP_848512.1:p.Arg755Cys
histone deacetylase 9 isoform 4 NP_848510.1:p.Arg752= NP_848510.1:p.Arg752Cys
histone deacetylase 9 isoform 11 NP_001308797.1:p.Arg730= NP_001308797.1:p.Arg730Cys
histone deacetylase 9 isoform 20 NP_001308806.1:p.Arg711= NP_001308806.1:p.Arg711Cys
histone deacetylase 9 isoform 20 NP_001308826.1:p.Arg711= NP_001308826.1:p.Arg711Cys
histone deacetylase 9 isoform 1 NP_478056.1:p.Arg752= NP_478056.1:p.Arg752Cys
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#.

3 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2736315813 Nov 08, 2017 (151)
2 GNOMAD ss4159290451 Apr 26, 2021 (155)
3 TOPMED ss4737490554 Apr 26, 2021 (155)
4 gnomAD - Genomes NC_000007.14 - 18793393 Apr 26, 2021 (155)
5 TopMed NC_000007.14 - 18793393 Apr 26, 2021 (155)
6 ALFA NC_000007.14 - 18793393 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
ss2736315813 NC_000007.13:18833015:C:T NC_000007.14:18793392:C:T (self)
254473747, 574868113, 5987912794, ss4159290451, ss4737490554 NC_000007.14:18793392:C:T NC_000007.14:18793392: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 rs1489191203

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.post820+afb47a3d