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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.

rs1491244881

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:32308956-32308957 (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
delGC
Variation Type
Deletion
Frequency
delGC=0.00000 (0/11862, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TSBP1 : Intron Variant
TSBP1-AS1 : Intron 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 11862 GC=1.00000 =0.00000 1.0 0.0 0.0 N/A
European Sub 7618 GC=1.0000 =0.0000 1.0 0.0 0.0 N/A
African Sub 2816 GC=1.0000 =0.0000 1.0 0.0 0.0 N/A
African Others Sub 108 GC=1.000 =0.000 1.0 0.0 0.0 N/A
African American Sub 2708 GC=1.0000 =0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 GC=1.000 =0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 GC=1.00 =0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 GC=1.00 =0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 GC=1.000 =0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 GC=1.000 =0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 GC=1.00 =0.00 1.0 0.0 0.0 N/A
Other Sub 470 GC=1.000 =0.000 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
Allele Frequency Aggregator Total Global 11862 GC=1.00000 delGC=0.00000
Allele Frequency Aggregator European Sub 7618 GC=1.0000 delGC=0.0000
Allele Frequency Aggregator African Sub 2816 GC=1.0000 delGC=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 GC=1.000 delGC=0.000
Allele Frequency Aggregator Other Sub 470 GC=1.000 delGC=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 GC=1.000 delGC=0.000
Allele Frequency Aggregator Asian Sub 108 GC=1.000 delGC=0.000
Allele Frequency Aggregator South Asian Sub 94 GC=1.00 delGC=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 6 NC_000006.12:g.32308956_32308957del
GRCh37.p13 chr 6 NC_000006.11:g.32276733_32276734del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.3747431_3747432del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.3747537_3747538del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.3532335_3532336del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.3537931_3537932del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.3550423_3550424del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.3556008_3556009del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.3625245_3625246del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.3624543_3624544del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.3613948_3613949del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.3619568_3619569del
Gene: TSBP1, testis expressed basic protein 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TSBP1 transcript variant 2 NM_001286474.2:c.575-6328…

NM_001286474.2:c.575-6328_575-6327del

N/A Intron Variant
TSBP1 transcript variant 3 NM_001286475.2:c.533-6328…

NM_001286475.2:c.533-6328_533-6327del

N/A Intron Variant
TSBP1 transcript variant 1 NM_006781.5:c.581-6328_58…

NM_006781.5:c.581-6328_581-6327del

N/A Intron Variant
TSBP1 transcript variant X1 XM_017010182.2:c.298+5657…

XM_017010182.2:c.298+5657_298+5658del

N/A Intron Variant
TSBP1 transcript variant X2 XM_024446307.2:c.712+5657…

XM_024446307.2:c.712+5657_712+5658del

N/A Intron Variant
Gene: TSBP1-AS1, TSBP1 and BTNL2 antisense RNA 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TSBP1-AS1 transcript variant 1 NR_136244.1:n. N/A Intron Variant
TSBP1-AS1 transcript variant 2 NR_136245.1:n. N/A Intron Variant
TSBP1-AS1 transcript variant 3 NR_136246.1:n. N/A Intron 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 GC= delGC
GRCh38.p14 chr 6 NC_000006.12:g.32308956_32308957= NC_000006.12:g.32308956_32308957del
GRCh37.p13 chr 6 NC_000006.11:g.32276733_32276734= NC_000006.11:g.32276733_32276734del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.3747431_3747432= NT_113891.3:g.3747431_3747432del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.3747537_3747538= NT_113891.2:g.3747537_3747538del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.3532335_3532336= NT_167248.2:g.3532335_3532336del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.3537931_3537932= NT_167248.1:g.3537931_3537932del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.3550423_3550424= NT_167245.2:g.3550423_3550424del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.3556008_3556009= NT_167245.1:g.3556008_3556009del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.3625245_3625246= NT_167249.2:g.3625245_3625246del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.3624543_3624544= NT_167249.1:g.3624543_3624544del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.3613948_3613949= NT_167246.2:g.3613948_3613949del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.3619568_3619569= NT_167246.1:g.3619568_3619569del
TSBP1 transcript variant 2 NM_001286474.2:c.575-6327= NM_001286474.2:c.575-6328_575-6327del
TSBP1 transcript variant 3 NM_001286475.2:c.533-6327= NM_001286475.2:c.533-6328_533-6327del
C6orf10 transcript NM_006781.3:c.581-6327= NM_006781.3:c.581-6328_581-6327del
TSBP1 transcript variant 1 NM_006781.5:c.581-6327= NM_006781.5:c.581-6328_581-6327del
C6orf10 transcript variant X1 XM_005248809.1:c.575-6327= XM_005248809.1:c.575-6328_575-6327del
C6orf10 transcript variant X2 XM_005248810.1:c.554-6327= XM_005248810.1:c.554-6328_554-6327del
C6orf10 transcript variant X1 XM_005272765.1:c.575-6337= XM_005272765.1:c.575-6338_575-6337del
C6orf10 transcript variant X2 XM_005272766.1:c.554-6337= XM_005272766.1:c.554-6338_554-6337del
C6orf10 transcript variant X1 XM_005274911.1:c.575-6335= XM_005274911.1:c.575-6336_575-6335del
C6orf10 transcript variant X2 XM_005274912.1:c.554-6335= XM_005274912.1:c.554-6336_554-6335del
C6orf10 transcript variant X1 XM_005275077.1:c.575-6327= XM_005275077.1:c.575-6328_575-6327del
C6orf10 transcript variant X2 XM_005275078.1:c.554-6327= XM_005275078.1:c.554-6328_554-6327del
C6orf10 transcript variant X1 XM_005275341.1:c.575-6323= XM_005275341.1:c.575-6324_575-6323del
C6orf10 transcript variant X2 XM_005275342.1:c.554-6323= XM_005275342.1:c.554-6324_554-6323del
C6orf10 transcript variant X1 XM_005275508.1:c.575-6329= XM_005275508.1:c.575-6330_575-6329del
C6orf10 transcript variant X2 XM_005275509.1:c.554-6329= XM_005275509.1:c.554-6330_554-6329del
TSBP1 transcript variant X1 XM_017010182.2:c.298+5658= XM_017010182.2:c.298+5657_298+5658del
TSBP1 transcript variant X2 XM_024446307.2:c.712+5658= XM_024446307.2:c.712+5657_712+5658del
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#.

1 Frequency submission
No Submitter Submission ID Date (Build)
1 ALFA NC_000006.12 - 32308956 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
6210324483 NC_000006.12:32308955:GC: NC_000006.12:32308955:GC: (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 rs1491244881

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