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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.

rs146866971

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr21:25736087-25736093 (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
dupT
Variation Type
Indel Insertion and Deletion
Frequency
dupT=0.007802 (2065/264690, TOPMED)
dupT=0.007556 (1058/140018, GnomAD)
dupT=0.00612 (86/14050, ALFA) (+ 1 more)
dupT=0.0080 (51/6404, 1000G_30x)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GABPA : Intron Variant
ATP5PF : 2KB Upstream 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 TTTTTTT=0.99388 TTTTTTTT=0.00612
European Sub 9690 TTTTTTT=1.0000 TTTTTTTT=0.0000
African Sub 2898 TTTTTTT=0.9727 TTTTTTTT=0.0273
African Others Sub 114 TTTTTTT=0.982 TTTTTTTT=0.018
African American Sub 2784 TTTTTTT=0.9723 TTTTTTTT=0.0277
Asian Sub 112 TTTTTTT=1.000 TTTTTTTT=0.000
East Asian Sub 86 TTTTTTT=1.00 TTTTTTTT=0.00
Other Asian Sub 26 TTTTTTT=1.00 TTTTTTTT=0.00
Latin American 1 Sub 146 TTTTTTT=0.986 TTTTTTTT=0.014
Latin American 2 Sub 610 TTTTTTT=1.000 TTTTTTTT=0.000
South Asian Sub 98 TTTTTTT=1.00 TTTTTTTT=0.00
Other Sub 496 TTTTTTT=0.990 TTTTTTTT=0.010


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 -

No frequency provided

dupT=0.007802
gnomAD - Genomes Global Study-wide 140018 -

No frequency provided

dupT=0.007556
gnomAD - Genomes European Sub 75794 -

No frequency provided

dupT=0.00007
gnomAD - Genomes African Sub 41994 -

No frequency provided

dupT=0.02379
gnomAD - Genomes American Sub 13624 -

No frequency provided

dupT=0.00279
gnomAD - Genomes Ashkenazi Jewish Sub 3322 -

No frequency provided

dupT=0.0000
gnomAD - Genomes East Asian Sub 3132 -

No frequency provided

dupT=0.0000
gnomAD - Genomes Other Sub 2152 -

No frequency provided

dupT=0.0074
Allele Frequency Aggregator Total Global 14050 (T)7=0.99388 dupT=0.00612
Allele Frequency Aggregator European Sub 9690 (T)7=1.0000 dupT=0.0000
Allele Frequency Aggregator African Sub 2898 (T)7=0.9727 dupT=0.0273
Allele Frequency Aggregator Latin American 2 Sub 610 (T)7=1.000 dupT=0.000
Allele Frequency Aggregator Other Sub 496 (T)7=0.990 dupT=0.010
Allele Frequency Aggregator Latin American 1 Sub 146 (T)7=0.986 dupT=0.014
Allele Frequency Aggregator Asian Sub 112 (T)7=1.000 dupT=0.000
Allele Frequency Aggregator South Asian Sub 98 (T)7=1.00 dupT=0.00
1000Genomes_30x Global Study-wide 6404 -

No frequency provided

dupT=0.0080
1000Genomes_30x African Sub 1786 -

No frequency provided

dupT=0.0269
1000Genomes_30x Europe Sub 1266 -

No frequency provided

dupT=0.0000
1000Genomes_30x South Asian Sub 1202 -

No frequency provided

dupT=0.0000
1000Genomes_30x East Asian Sub 1170 -

No frequency provided

dupT=0.0000
1000Genomes_30x American Sub 980 -

No frequency provided

dupT=0.003
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 21 NC_000021.9:g.25736093dup
GRCh37.p13 chr 21 NC_000021.8:g.27108404dup
Gene: GABPA, GA binding protein transcription factor subunit alpha (plus strand)
Molecule type Change Amino acid[Codon] SO Term
GABPA transcript variant 2 NM_001197297.2:c.-27+1023…

NM_001197297.2:c.-27+1023dup

N/A Intron Variant
GABPA transcript variant 1 NM_002040.4:c.-27+515dup N/A Intron Variant
GABPA transcript variant X3 XM_005260938.6:c.-27+708d…

XM_005260938.6:c.-27+708dup

N/A Intron Variant
GABPA transcript variant X2 XM_017028313.3:c.-39+515d…

XM_017028313.3:c.-39+515dup

N/A Intron Variant
GABPA transcript variant X1 XM_024452062.2:c.-180+708…

XM_024452062.2:c.-180+708dup

N/A Intron Variant
GABPA transcript variant X4 XM_047440737.1:c.-192+708…

XM_047440737.1:c.-192+708dup

N/A Intron Variant
GABPA transcript variant X5 XM_047440738.1:c.-271+708…

XM_047440738.1:c.-271+708dup

N/A Intron Variant
GABPA transcript variant X6 XM_047440739.1:c.-118+708…

XM_047440739.1:c.-118+708dup

N/A Intron Variant
Gene: ATP5PF, ATP synthase peripheral stalk subunit F6 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
ATP5PF transcript variant 3 NM_001003696.2:c. N/A Upstream Transcript Variant
ATP5PF transcript variant 4 NM_001003697.2:c. N/A Upstream Transcript Variant
ATP5PF transcript variant 5 NM_001003701.2:c. N/A Upstream Transcript Variant
ATP5PF transcript variant 1 NM_001003703.2:c. N/A Upstream Transcript Variant
ATP5PF transcript variant 6 NM_001320266.2:c. N/A Upstream Transcript Variant
ATP5PF transcript variant 7 NM_001320267.2:c. N/A Upstream Transcript Variant
ATP5PF transcript variant 2 NM_001685.5:c. N/A Upstream 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 (T)7= dupT
GRCh38.p14 chr 21 NC_000021.9:g.25736087_25736093= NC_000021.9:g.25736093dup
GRCh37.p13 chr 21 NC_000021.8:g.27108398_27108404= NC_000021.8:g.27108404dup
GABPA transcript variant 2 NM_001197297.1:c.-27+1017= NM_001197297.1:c.-27+1023dup
GABPA transcript variant 2 NM_001197297.2:c.-27+1017= NM_001197297.2:c.-27+1023dup
GABPA transcript variant 1 NM_002040.3:c.-27+509= NM_002040.3:c.-27+515dup
GABPA transcript variant 1 NM_002040.4:c.-27+509= NM_002040.4:c.-27+515dup
GABPA transcript variant X1 XM_005260938.1:c.-27+702= XM_005260938.1:c.-27+708dup
GABPA transcript variant X3 XM_005260938.6:c.-27+702= XM_005260938.6:c.-27+708dup
GABPA transcript variant X2 XM_017028313.3:c.-39+509= XM_017028313.3:c.-39+515dup
GABPA transcript variant X1 XM_024452062.2:c.-180+702= XM_024452062.2:c.-180+708dup
GABPA transcript variant X4 XM_047440737.1:c.-192+702= XM_047440737.1:c.-192+708dup
GABPA transcript variant X5 XM_047440738.1:c.-271+702= XM_047440738.1:c.-271+708dup
GABPA transcript variant X6 XM_047440739.1:c.-118+702= XM_047440739.1:c.-118+708dup
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#.

12 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss328311958 May 09, 2011 (134)
2 1000GENOMES ss499779442 May 04, 2012 (137)
3 LUNTER ss553104408 Apr 25, 2013 (138)
4 GNOMAD ss2970827695 Nov 08, 2017 (151)
5 MCHAISSO ss3065836797 Nov 08, 2017 (151)
6 TOPMED ss5098628951 Apr 26, 2021 (155)
7 1000G_HIGH_COVERAGE ss5309913490 Oct 13, 2022 (156)
8 HUGCELL_USP ss5501987212 Oct 13, 2022 (156)
9 1000G_HIGH_COVERAGE ss5616910742 Oct 13, 2022 (156)
10 SANFORD_IMAGENETICS ss5663834342 Oct 13, 2022 (156)
11 EVA ss5892003179 Oct 13, 2022 (156)
12 EVA ss5958723830 Oct 13, 2022 (156)
13 1000Genomes_30x NC_000021.9 - 25736087 Oct 13, 2022 (156)
14 gnomAD - Genomes NC_000021.9 - 25736087 Apr 26, 2021 (155)
15 TopMed NC_000021.9 - 25736087 Apr 26, 2021 (155)
16 ALFA NC_000021.9 - 25736087 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
ss328311958, ss553104408 NC_000021.7:26030268::T NC_000021.9:25736086:TTTTTTT:TTTTT…

NC_000021.9:25736086:TTTTTTT:TTTTTTTT

(self)
ss499779442, ss2970827695, ss5663834342, ss5958723830 NC_000021.8:27108397::T NC_000021.9:25736086:TTTTTTT:TTTTT…

NC_000021.9:25736086:TTTTTTT:TTTTTTTT

(self)
104436677, 560753567, 373737897, ss3065836797, ss5098628951, ss5309913490, ss5501987212, ss5616910742, ss5892003179 NC_000021.9:25736086::T NC_000021.9:25736086:TTTTTTT:TTTTT…

NC_000021.9:25736086:TTTTTTT:TTTTTTTT

(self)
8936190835 NC_000021.9:25736086:TTTTTTT:TTTTT…

NC_000021.9:25736086:TTTTTTT:TTTTTTTT

NC_000021.9:25736086:TTTTTTT:TTTTT…

NC_000021.9:25736086:TTTTTTT:TTTTTTTT

(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 rs146866971

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