Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs1482027580

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr8:28835327 (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 / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000004 (1/264690, TOPMED)
A=0.000004 (1/250884, GnomAD_exome)
T=0.00003 (1/32058, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
INTS9 : 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 32058 C=0.99997 T=0.00003 0.999938 0.0 6.2e-05 0
European Sub 23856 C=0.99996 T=0.00004 0.999916 0.0 0.000084 0
African Sub 2314 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Others Sub 84 C=1.00 T=0.00 1.0 0.0 0.0 N/A
African American Sub 2230 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 C=1.000 T=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 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 94 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Sub 4558 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=0.999996 T=0.000004
gnomAD - Exomes Global Study-wide 250884 C=0.999996 A=0.000004
gnomAD - Exomes European Sub 134978 C=1.000000 A=0.000000
gnomAD - Exomes Asian Sub 48966 C=1.00000 A=0.00000
gnomAD - Exomes American Sub 34518 C=0.99997 A=0.00003
gnomAD - Exomes African Sub 16248 C=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10062 C=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6112 C=1.0000 A=0.0000
Allele Frequency Aggregator Total Global 32058 C=0.99997 T=0.00003
Allele Frequency Aggregator European Sub 23856 C=0.99996 T=0.00004
Allele Frequency Aggregator Other Sub 4558 C=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 2314 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 108 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 94 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 8 NC_000008.11:g.28835327C>A
GRCh38.p14 chr 8 NC_000008.11:g.28835327C>T
GRCh37.p13 chr 8 NC_000008.10:g.28692844C>A
GRCh37.p13 chr 8 NC_000008.10:g.28692844C>T
INTS9 RefSeqGene NG_016981.2:g.59855G>T
INTS9 RefSeqGene NG_016981.2:g.59855G>A
Gene: INTS9, integrator complex subunit 9 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
INTS9 transcript variant 1 NM_018250.4:c.453G>T Q [CAG] > H [CAT] Coding Sequence Variant
integrator complex subunit 9 isoform 1 NP_060720.2:p.Gln151His Q (Gln) > H (His) Missense Variant
INTS9 transcript variant 1 NM_018250.4:c.453G>A Q [CAG] > Q [CAA] Coding Sequence Variant
integrator complex subunit 9 isoform 1 NP_060720.2:p.Gln151= Q (Gln) > Q (Gln) Synonymous Variant
INTS9 transcript variant 5 NM_001363038.2:c.453G>T Q [CAG] > H [CAT] Coding Sequence Variant
integrator complex subunit 9 isoform 4 NP_001349967.1:p.Gln151His Q (Gln) > H (His) Missense Variant
INTS9 transcript variant 5 NM_001363038.2:c.453G>A Q [CAG] > Q [CAA] Coding Sequence Variant
integrator complex subunit 9 isoform 4 NP_001349967.1:p.Gln151= Q (Gln) > Q (Gln) Synonymous Variant
INTS9 transcript variant 2 NM_001145159.3:c.390G>T Q [CAG] > H [CAT] Coding Sequence Variant
integrator complex subunit 9 isoform 2 NP_001138631.1:p.Gln130His Q (Gln) > H (His) Missense Variant
INTS9 transcript variant 2 NM_001145159.3:c.390G>A Q [CAG] > Q [CAA] Coding Sequence Variant
integrator complex subunit 9 isoform 2 NP_001138631.1:p.Gln130= Q (Gln) > Q (Gln) Synonymous Variant
INTS9 transcript variant 4 NM_001172562.2:c.381G>T Q [CAG] > H [CAT] Coding Sequence Variant
integrator complex subunit 9 isoform 3 NP_001166033.1:p.Gln127His Q (Gln) > H (His) Missense Variant
INTS9 transcript variant 4 NM_001172562.2:c.381G>A Q [CAG] > Q [CAA] Coding Sequence Variant
integrator complex subunit 9 isoform 3 NP_001166033.1:p.Gln127= Q (Gln) > Q (Gln) Synonymous Variant
INTS9 transcript variant 3 NR_026826.3:n.349G>T N/A Non Coding Transcript Variant
INTS9 transcript variant 3 NR_026826.3:n.349G>A N/A Non Coding Transcript Variant
INTS9 transcript variant X3 XM_011544574.1:c.381G>T Q [CAG] > H [CAT] Coding Sequence Variant
integrator complex subunit 9 isoform X2 XP_011542876.1:p.Gln127His Q (Gln) > H (His) Missense Variant
INTS9 transcript variant X3 XM_011544574.1:c.381G>A Q [CAG] > Q [CAA] Coding Sequence Variant
integrator complex subunit 9 isoform X2 XP_011542876.1:p.Gln127= Q (Gln) > Q (Gln) Synonymous Variant
INTS9 transcript variant X1 XM_011544573.2:c.390G>T Q [CAG] > H [CAT] Coding Sequence Variant
integrator complex subunit 9 isoform X1 XP_011542875.1:p.Gln130His Q (Gln) > H (His) Missense Variant
INTS9 transcript variant X1 XM_011544573.2:c.390G>A Q [CAG] > Q [CAA] Coding Sequence Variant
integrator complex subunit 9 isoform X1 XP_011542875.1:p.Gln130= Q (Gln) > Q (Gln) Synonymous Variant
INTS9 transcript variant X2 XM_011544575.3:c.381G>T Q [CAG] > H [CAT] Coding Sequence Variant
integrator complex subunit 9 isoform X2 XP_011542877.1:p.Gln127His Q (Gln) > H (His) Missense Variant
INTS9 transcript variant X2 XM_011544575.3:c.381G>A Q [CAG] > Q [CAA] Coding Sequence Variant
integrator complex subunit 9 isoform X2 XP_011542877.1:p.Gln127= Q (Gln) > Q (Gln) Synonymous Variant
INTS9 transcript variant X4 XM_006716357.5:c.453G>T Q [CAG] > H [CAT] Coding Sequence Variant
integrator complex subunit 9 isoform X3 XP_006716420.1:p.Gln151His Q (Gln) > H (His) Missense Variant
INTS9 transcript variant X4 XM_006716357.5:c.453G>A Q [CAG] > Q [CAA] Coding Sequence Variant
integrator complex subunit 9 isoform X3 XP_006716420.1:p.Gln151= Q (Gln) > Q (Gln) Synonymous Variant
INTS9 transcript variant X5 XM_011544576.3:c.453G>T Q [CAG] > H [CAT] Coding Sequence Variant
integrator complex subunit 9 isoform X4 XP_011542878.1:p.Gln151His Q (Gln) > H (His) Missense Variant
INTS9 transcript variant X5 XM_011544576.3:c.453G>A Q [CAG] > Q [CAA] Coding Sequence Variant
integrator complex subunit 9 isoform X4 XP_011542878.1:p.Gln151= Q (Gln) > Q (Gln) Synonymous Variant
INTS9 transcript variant X6 XM_047421954.1:c.390G>T Q [CAG] > H [CAT] Coding Sequence Variant
integrator complex subunit 9 isoform X5 XP_047277910.1:p.Gln130His Q (Gln) > H (His) Missense Variant
INTS9 transcript variant X6 XM_047421954.1:c.390G>A Q [CAG] > Q [CAA] Coding Sequence Variant
integrator complex subunit 9 isoform X5 XP_047277910.1:p.Gln130= Q (Gln) > Q (Gln) Synonymous Variant
INTS9 transcript variant X7 XM_047421955.1:c.453G>T Q [CAG] > H [CAT] Coding Sequence Variant
integrator complex subunit 9 isoform X6 XP_047277911.1:p.Gln151His Q (Gln) > H (His) Missense Variant
INTS9 transcript variant X7 XM_047421955.1:c.453G>A Q [CAG] > Q [CAA] Coding Sequence Variant
integrator complex subunit 9 isoform X6 XP_047277911.1:p.Gln151= Q (Gln) > Q (Gln) Synonymous Variant
INTS9 transcript variant X8 XM_047421956.1:c.390G>T Q [CAG] > H [CAT] Coding Sequence Variant
integrator complex subunit 9 isoform X7 XP_047277912.1:p.Gln130His Q (Gln) > H (His) Missense Variant
INTS9 transcript variant X8 XM_047421956.1:c.390G>A Q [CAG] > Q [CAA] Coding Sequence Variant
integrator complex subunit 9 isoform X7 XP_047277912.1:p.Gln130= Q (Gln) > Q (Gln) Synonymous Variant
INTS9 transcript variant X9 XM_047421957.1:c.453G>T Q [CAG] > H [CAT] Coding Sequence Variant
integrator complex subunit 9 isoform X8 XP_047277913.1:p.Gln151His Q (Gln) > H (His) Missense Variant
INTS9 transcript variant X9 XM_047421957.1:c.453G>A Q [CAG] > Q [CAA] Coding Sequence Variant
integrator complex subunit 9 isoform X8 XP_047277913.1:p.Gln151= Q (Gln) > Q (Gln) Synonymous Variant
INTS9 transcript variant X10 XM_047421958.1:c.390G>T Q [CAG] > H [CAT] Coding Sequence Variant
integrator complex subunit 9 isoform X9 XP_047277914.1:p.Gln130His Q (Gln) > H (His) Missense Variant
INTS9 transcript variant X10 XM_047421958.1:c.390G>A Q [CAG] > Q [CAA] Coding Sequence Variant
integrator complex subunit 9 isoform X9 XP_047277914.1:p.Gln130= Q (Gln) > Q (Gln) 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= A T
GRCh38.p14 chr 8 NC_000008.11:g.28835327= NC_000008.11:g.28835327C>A NC_000008.11:g.28835327C>T
GRCh37.p13 chr 8 NC_000008.10:g.28692844= NC_000008.10:g.28692844C>A NC_000008.10:g.28692844C>T
INTS9 RefSeqGene NG_016981.2:g.59855= NG_016981.2:g.59855G>T NG_016981.2:g.59855G>A
INTS9 transcript variant 1 NM_018250.4:c.453= NM_018250.4:c.453G>T NM_018250.4:c.453G>A
INTS9 transcript variant 1 NM_018250.3:c.453= NM_018250.3:c.453G>T NM_018250.3:c.453G>A
INTS9 transcript variant 2 NM_001145159.3:c.390= NM_001145159.3:c.390G>T NM_001145159.3:c.390G>A
INTS9 transcript variant 2 NM_001145159.2:c.390= NM_001145159.2:c.390G>T NM_001145159.2:c.390G>A
INTS9 transcript variant 3 NR_026826.3:n.349= NR_026826.3:n.349G>T NR_026826.3:n.349G>A
INTS9 transcript variant 3 NR_026826.2:n.561= NR_026826.2:n.561G>T NR_026826.2:n.561G>A
INTS9 transcript variant 5 NM_001363038.2:c.453= NM_001363038.2:c.453G>T NM_001363038.2:c.453G>A
INTS9 transcript variant 5 NM_001363038.1:c.453= NM_001363038.1:c.453G>T NM_001363038.1:c.453G>A
INTS9 transcript variant 4 NM_001172562.2:c.381= NM_001172562.2:c.381G>T NM_001172562.2:c.381G>A
INTS9 transcript variant 4 NM_001172562.1:c.381= NM_001172562.1:c.381G>T NM_001172562.1:c.381G>A
INTS9 transcript variant X4 XM_006716357.5:c.453= XM_006716357.5:c.453G>T XM_006716357.5:c.453G>A
INTS9 transcript variant X5 XM_006716357.4:c.453= XM_006716357.4:c.453G>T XM_006716357.4:c.453G>A
INTS9 transcript variant X5 XM_006716357.3:c.453= XM_006716357.3:c.453G>T XM_006716357.3:c.453G>A
INTS9 transcript variant X5 XM_006716357.2:c.453= XM_006716357.2:c.453G>T XM_006716357.2:c.453G>A
INTS9 transcript variant X6 XM_006716357.1:c.453= XM_006716357.1:c.453G>T XM_006716357.1:c.453G>A
INTS9 transcript variant X2 XM_011544575.3:c.381= XM_011544575.3:c.381G>T XM_011544575.3:c.381G>A
INTS9 transcript variant X4 XM_011544575.2:c.381= XM_011544575.2:c.381G>T XM_011544575.2:c.381G>A
INTS9 transcript variant X4 XM_011544575.1:c.381= XM_011544575.1:c.381G>T XM_011544575.1:c.381G>A
INTS9 transcript variant X5 XM_011544576.3:c.453= XM_011544576.3:c.453G>T XM_011544576.3:c.453G>A
INTS9 transcript variant X6 XM_011544576.2:c.453= XM_011544576.2:c.453G>T XM_011544576.2:c.453G>A
INTS9 transcript variant X6 XM_011544576.1:c.453= XM_011544576.1:c.453G>T XM_011544576.1:c.453G>A
INTS9 transcript variant X1 XM_011544573.2:c.390= XM_011544573.2:c.390G>T XM_011544573.2:c.390G>A
INTS9 transcript variant X2 XM_011544573.1:c.390= XM_011544573.1:c.390G>T XM_011544573.1:c.390G>A
INTS9 transcript variant X6 XM_047421954.1:c.390= XM_047421954.1:c.390G>T XM_047421954.1:c.390G>A
INTS9 transcript variant X9 XM_047421957.1:c.453= XM_047421957.1:c.453G>T XM_047421957.1:c.453G>A
INTS9 transcript variant X3 XM_011544574.1:c.381= XM_011544574.1:c.381G>T XM_011544574.1:c.381G>A
INTS9 transcript variant X7 XM_047421955.1:c.453= XM_047421955.1:c.453G>T XM_047421955.1:c.453G>A
INTS9 transcript variant X8 XM_047421956.1:c.390= XM_047421956.1:c.390G>T XM_047421956.1:c.390G>A
INTS9 transcript variant X10 XM_047421958.1:c.390= XM_047421958.1:c.390G>T XM_047421958.1:c.390G>A
integrator complex subunit 9 isoform 1 NP_060720.2:p.Gln151= NP_060720.2:p.Gln151His NP_060720.2:p.Gln151=
integrator complex subunit 9 isoform 2 NP_001138631.1:p.Gln130= NP_001138631.1:p.Gln130His NP_001138631.1:p.Gln130=
integrator complex subunit 9 isoform 4 NP_001349967.1:p.Gln151= NP_001349967.1:p.Gln151His NP_001349967.1:p.Gln151=
integrator complex subunit 9 isoform 3 NP_001166033.1:p.Gln127= NP_001166033.1:p.Gln127His NP_001166033.1:p.Gln127=
integrator complex subunit 9 isoform X3 XP_006716420.1:p.Gln151= XP_006716420.1:p.Gln151His XP_006716420.1:p.Gln151=
integrator complex subunit 9 isoform X2 XP_011542877.1:p.Gln127= XP_011542877.1:p.Gln127His XP_011542877.1:p.Gln127=
integrator complex subunit 9 isoform X4 XP_011542878.1:p.Gln151= XP_011542878.1:p.Gln151His XP_011542878.1:p.Gln151=
integrator complex subunit 9 isoform X1 XP_011542875.1:p.Gln130= XP_011542875.1:p.Gln130His XP_011542875.1:p.Gln130=
integrator complex subunit 9 isoform X5 XP_047277910.1:p.Gln130= XP_047277910.1:p.Gln130His XP_047277910.1:p.Gln130=
integrator complex subunit 9 isoform X8 XP_047277913.1:p.Gln151= XP_047277913.1:p.Gln151His XP_047277913.1:p.Gln151=
integrator complex subunit 9 isoform X2 XP_011542876.1:p.Gln127= XP_011542876.1:p.Gln127His XP_011542876.1:p.Gln127=
integrator complex subunit 9 isoform X6 XP_047277911.1:p.Gln151= XP_047277911.1:p.Gln151His XP_047277911.1:p.Gln151=
integrator complex subunit 9 isoform X7 XP_047277912.1:p.Gln130= XP_047277912.1:p.Gln130His XP_047277912.1:p.Gln130=
integrator complex subunit 9 isoform X9 XP_047277914.1:p.Gln130= XP_047277914.1:p.Gln130His XP_047277914.1:p.Gln130=
INTS9 transcript variant X3 XM_005273567.1:c.61-21752= XM_005273567.1:c.61-21752G>T XM_005273567.1:c.61-21752G>A
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#.

2 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2737081974 Nov 08, 2017 (151)
2 TOPMED ss4780418874 Apr 26, 2021 (155)
3 gnomAD - Exomes NC_000008.10 - 28692844 Jul 13, 2019 (153)
4 TopMed NC_000008.11 - 28835327 Apr 26, 2021 (155)
5 ALFA NC_000008.11 - 28835327 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
6252316, ss2737081974 NC_000008.10:28692843:C:A NC_000008.11:28835326:C:A (self)
617796434, 7329203092, ss4780418874 NC_000008.11:28835326:C:T NC_000008.11:28835326: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 rs1482027580

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