Name: rs1478427793
Published: September 21, 2022
License: Open Access

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.

rs1478427793

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr7:18128825 (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: dupG
Variation Type: Indel Insertion and Deletion
Frequency: dupG=0.000007 (1/140138, GnomAD)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: HDAC9 : Intron Variant
MIR1302-6 : 2KB Upstream Variant
Publications: 0 citations
Genomic View: See rs on genome

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
gnomAD - Genomes	Global	Study-wide	140138	- No frequency provided	dupG=0.000007
gnomAD - Genomes	European	Sub	75904	- No frequency provided	dupG=0.00001
gnomAD - Genomes	African	Sub	42014	- No frequency provided	dupG=0.00000
gnomAD - Genomes	American	Sub	13630	- No frequency provided	dupG=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	- No frequency provided	dupG=0.0000
gnomAD - Genomes	East Asian	Sub	3118	- No frequency provided	dupG=0.0000
gnomAD - Genomes	Other	Sub	2154	- No frequency provided	dupG=0.0000

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.18128825dup
GRCh37.p13 chr 7	NC_000007.13:g.18168448dup
HDAC9 RefSeqGene	NG_023250.3:g.46877dup

Gene: HDAC9, histone deacetylase 9 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
HDAC9 transcript variant 6	NM_001204144.3:c.-96-3340… NM_001204144.3:c.-96-33404dup	N/A	Intron Variant
HDAC9 transcript variant 11	NM_001321868.2:c.-96-3340… NM_001321868.2:c.-96-33404dup	N/A	Intron Variant
HDAC9 transcript variant 12	NM_001321869.2:c.-96-3340… NM_001321869.2:c.-96-33404dup	N/A	Intron Variant
HDAC9 transcript variant 13	NM_001321870.2:c.-96-3340… NM_001321870.2:c.-96-33404dup	N/A	Intron Variant
HDAC9 transcript variant 14	NM_001321871.2:c.-96-3340… NM_001321871.2:c.-96-33404dup	N/A	Intron Variant
HDAC9 transcript variant 15	NM_001321872.2:c.-96-3340… NM_001321872.2:c.-96-33404dup	N/A	Intron Variant
HDAC9 transcript variant 16	NM_001321873.2:c.-96-3340… NM_001321873.2:c.-96-33404dup	N/A	Intron Variant
HDAC9 transcript variant 7	NM_001204145.3:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 8	NM_001204146.2:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 9	NM_001204147.3:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 10	NM_001204148.3:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 17	NM_001321874.2:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 18	NM_001321875.2:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 19	NM_001321876.2:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 20	NM_001321877.2:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 21	NM_001321878.2:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 22	NM_001321879.2:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 23	NM_001321884.2:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 24	NM_001321885.2:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 25	NM_001321886.2:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 26	NM_001321887.2:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 27	NM_001321888.2:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 28	NM_001321889.2:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 29	NM_001321890.2:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 30	NM_001321891.2:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 31	NM_001321893.2:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 32	NM_001321894.2:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 33	NM_001321895.2:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 34	NM_001321896.2:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 35	NM_001321897.2:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 36	NM_001321898.2:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 37	NM_001321899.2:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 38	NM_001321900.2:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 39	NM_001321901.2:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 40	NM_001321902.2:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 3	NM_014707.4:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 1	NM_058176.2:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 4	NM_178423.3:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 5	NM_178425.4:c.	N/A	Genic Upstream Transcript Variant
HDAC9 transcript variant 41	NR_135835.2:n.	N/A	Genic Upstream Transcript Variant

Gene: MIR1302-6, microRNA 1302-6 (minus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
MIR1302-6 transcript	NR_031635.1:n.	N/A	Upstream Transcript Variant

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

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=	dupG
GRCh38.p14 chr 7	NC_000007.14:g.18128825=	NC_000007.14:g.18128825dup
GRCh37.p13 chr 7	NC_000007.13:g.18168448=	NC_000007.13:g.18168448dup
HDAC9 RefSeqGene	NG_023250.3:g.46877=	NG_023250.3:g.46877dup
HDAC9 transcript variant 6	NM_001204144.1:c.-96-33404=	NM_001204144.1:c.-96-33404dup
HDAC9 transcript variant 6	NM_001204144.3:c.-96-33404=	NM_001204144.3:c.-96-33404dup
HDAC9 transcript variant 11	NM_001321868.2:c.-96-33404=	NM_001321868.2:c.-96-33404dup
HDAC9 transcript variant 12	NM_001321869.2:c.-96-33404=	NM_001321869.2:c.-96-33404dup
HDAC9 transcript variant 13	NM_001321870.2:c.-96-33404=	NM_001321870.2:c.-96-33404dup
HDAC9 transcript variant 14	NM_001321871.2:c.-96-33404=	NM_001321871.2:c.-96-33404dup
HDAC9 transcript variant 15	NM_001321872.2:c.-96-33404=	NM_001321872.2:c.-96-33404dup
HDAC9 transcript variant 16	NM_001321873.2:c.-96-33404=	NM_001321873.2:c.-96-33404dup
HDAC9 transcript variant X1	XM_005249913.1:c.-96-33404=	XM_005249913.1:c.-96-33404dup

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#.

1 SubSNP, 1 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss2850323506	Nov 08, 2017 (151)
2	gnomAD - Genomes	NC_000007.14 - 18128825	Apr 26, 2021 (155)

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
ss2850323506	NC_000007.13:18168447::G	NC_000007.14:18128824:G:GG	(self)
254324861	NC_000007.14:18128824::G	NC_000007.14:18128824:G:GG	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs1478427793

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1478427793