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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.

rs1491330382

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:33260624-33260630 (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
del(T)4 / delT / dupT
Variation Type
Indel Insertion and Deletion
Frequency
del(T)4=0.000007 (1/140122, GnomAD)
del(T)4=0.00000 (0/14050, ALFA)
dupT=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
VPS52 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
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
gnomAD - Genomes Global Study-wide 140122 (T)7=0.999993 del(T)4=0.000007
gnomAD - Genomes European Sub 75906 (T)7=1.00000 del(T)4=0.00000
gnomAD - Genomes African Sub 41990 (T)7=1.00000 del(T)4=0.00000
gnomAD - Genomes American Sub 13624 (T)7=0.99993 del(T)4=0.00007
gnomAD - Genomes Ashkenazi Jewish Sub 3324 (T)7=1.0000 del(T)4=0.0000
gnomAD - Genomes East Asian Sub 3134 (T)7=1.0000 del(T)4=0.0000
gnomAD - Genomes Other Sub 2144 (T)7=1.0000 del(T)4=0.0000
Allele Frequency Aggregator Total Global 14050 (T)7=1.00000 del(T)4=0.00000, dupT=0.00000
Allele Frequency Aggregator European Sub 9690 (T)7=1.0000 del(T)4=0.0000, dupT=0.0000
Allele Frequency Aggregator African Sub 2898 (T)7=1.0000 del(T)4=0.0000, dupT=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 (T)7=1.000 del(T)4=0.000, dupT=0.000
Allele Frequency Aggregator Other Sub 496 (T)7=1.000 del(T)4=0.000, dupT=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 (T)7=1.000 del(T)4=0.000, dupT=0.000
Allele Frequency Aggregator Asian Sub 112 (T)7=1.000 del(T)4=0.000, dupT=0.000
Allele Frequency Aggregator South Asian Sub 98 (T)7=1.00 del(T)4=0.00, dupT=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.33260627_33260630del
GRCh38.p14 chr 6 NC_000006.12:g.33260630del
GRCh38.p14 chr 6 NC_000006.12:g.33260630dup
GRCh37.p13 chr 6 NC_000006.11:g.33228404_33228407del
GRCh37.p13 chr 6 NC_000006.11:g.33228407del
GRCh37.p13 chr 6 NC_000006.11:g.33228407dup
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.4672106_4672109del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.4672109del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.4672109dup
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.4672212_4672215del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.4672215del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.4672215dup
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.4455029_4455032del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.4455032del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.4455032dup
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.4460625_4460628del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.4460628del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.4460628dup
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.4504140_4504143del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.4504143del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.4504143dup
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.4509725_4509728del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.4509728del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.4509728dup
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.4709294_4709297del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.4709297del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.4709297dup
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.4708592_4708595del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.4708595del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.4708595dup
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.4696572_4696575del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.4696575del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.4696575dup
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.4702157_4702160del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.4702160del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.4702160dup
Gene: VPS52, VPS52 subunit of GARP complex (minus strand)
Molecule type Change Amino acid[Codon] SO Term
VPS52 transcript variant 2 NM_001289174.2:c.1593+285…

NM_001289174.2:c.1593+2857_1593+2860del

N/A Intron Variant
VPS52 transcript variant 3 NM_001289175.1:c.1419+285…

NM_001289175.1:c.1419+2857_1419+2860del

N/A Intron Variant
VPS52 transcript variant 4 NM_001289176.1:c.1227+285…

NM_001289176.1:c.1227+2857_1227+2860del

N/A Intron Variant
VPS52 transcript variant 1 NM_022553.6:c.1794+2857_1…

NM_022553.6:c.1794+2857_1794+2860del

N/A Intron Variant
VPS52 transcript variant X3 XM_011514797.2:c.1593+285…

XM_011514797.2:c.1593+2857_1593+2860del

N/A Intron Variant
VPS52 transcript variant X1 XM_011514798.3:c.1593+285…

XM_011514798.3:c.1593+2857_1593+2860del

N/A Intron Variant
VPS52 transcript variant X2 XM_011514799.2:c.1593+285…

XM_011514799.2:c.1593+2857_1593+2860del

N/A Intron Variant
VPS52 transcript variant X4 XM_017011179.3:c. 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 (T)7= del(T)4 delT dupT
GRCh38.p14 chr 6 NC_000006.12:g.33260624_33260630= NC_000006.12:g.33260627_33260630del NC_000006.12:g.33260630del NC_000006.12:g.33260630dup
GRCh37.p13 chr 6 NC_000006.11:g.33228401_33228407= NC_000006.11:g.33228404_33228407del NC_000006.11:g.33228407del NC_000006.11:g.33228407dup
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.4672103_4672109= NT_113891.3:g.4672106_4672109del NT_113891.3:g.4672109del NT_113891.3:g.4672109dup
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.4672209_4672215= NT_113891.2:g.4672212_4672215del NT_113891.2:g.4672215del NT_113891.2:g.4672215dup
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.4455026_4455032= NT_167248.2:g.4455029_4455032del NT_167248.2:g.4455032del NT_167248.2:g.4455032dup
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.4460622_4460628= NT_167248.1:g.4460625_4460628del NT_167248.1:g.4460628del NT_167248.1:g.4460628dup
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.4504137_4504143= NT_167245.2:g.4504140_4504143del NT_167245.2:g.4504143del NT_167245.2:g.4504143dup
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.4509722_4509728= NT_167245.1:g.4509725_4509728del NT_167245.1:g.4509728del NT_167245.1:g.4509728dup
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.4709291_4709297= NT_167249.2:g.4709294_4709297del NT_167249.2:g.4709297del NT_167249.2:g.4709297dup
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.4708589_4708595= NT_167249.1:g.4708592_4708595del NT_167249.1:g.4708595del NT_167249.1:g.4708595dup
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.4696569_4696575= NT_167247.2:g.4696572_4696575del NT_167247.2:g.4696575del NT_167247.2:g.4696575dup
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.4702154_4702160= NT_167247.1:g.4702157_4702160del NT_167247.1:g.4702160del NT_167247.1:g.4702160dup
VPS52 transcript variant 2 NM_001289174.2:c.1593+2860= NM_001289174.2:c.1593+2857_1593+2860del NM_001289174.2:c.1593+2860del NM_001289174.2:c.1593+2860dup
VPS52 transcript variant 3 NM_001289175.1:c.1419+2860= NM_001289175.1:c.1419+2857_1419+2860del NM_001289175.1:c.1419+2860del NM_001289175.1:c.1419+2860dup
VPS52 transcript variant 4 NM_001289176.1:c.1227+2860= NM_001289176.1:c.1227+2857_1227+2860del NM_001289176.1:c.1227+2860del NM_001289176.1:c.1227+2860dup
VPS52 transcript NM_022553.4:c.1794+2860= NM_022553.4:c.1794+2857_1794+2860del NM_022553.4:c.1794+2860del NM_022553.4:c.1794+2860dup
VPS52 transcript variant 1 NM_022553.6:c.1794+2860= NM_022553.6:c.1794+2857_1794+2860del NM_022553.6:c.1794+2860del NM_022553.6:c.1794+2860dup
VPS52 transcript variant X1 XM_005249281.1:c.1593+2860= XM_005249281.1:c.1593+2857_1593+2860del XM_005249281.1:c.1593+2860del XM_005249281.1:c.1593+2860dup
VPS52 transcript variant X2 XM_005249282.1:c.1593+2860= XM_005249282.1:c.1593+2857_1593+2860del XM_005249282.1:c.1593+2860del XM_005249282.1:c.1593+2860dup
VPS52 transcript variant X3 XM_005249283.1:c.1419+2860= XM_005249283.1:c.1419+2857_1419+2860del XM_005249283.1:c.1419+2860del XM_005249283.1:c.1419+2860dup
VPS52 transcript variant X4 XM_005249284.1:c.1227+2860= XM_005249284.1:c.1227+2857_1227+2860del XM_005249284.1:c.1227+2860del XM_005249284.1:c.1227+2860dup
VPS52 transcript variant X1 XM_005272857.1:c.1593+2862= XM_005272857.1:c.1593+2859_1593+2862del XM_005272857.1:c.1593+2862del XM_005272857.1:c.1593+2862dup
VPS52 transcript variant X2 XM_005272858.1:c.1593+2862= XM_005272858.1:c.1593+2859_1593+2862del XM_005272858.1:c.1593+2862del XM_005272858.1:c.1593+2862dup
VPS52 transcript variant X3 XM_005272859.1:c.1419+2862= XM_005272859.1:c.1419+2859_1419+2862del XM_005272859.1:c.1419+2862del XM_005272859.1:c.1419+2862dup
VPS52 transcript variant X4 XM_005272860.1:c.1227+2862= XM_005272860.1:c.1227+2859_1227+2862del XM_005272860.1:c.1227+2862del XM_005272860.1:c.1227+2862dup
VPS52 transcript variant X1 XM_005275010.1:c.1593+2861= XM_005275010.1:c.1593+2858_1593+2861del XM_005275010.1:c.1593+2861del XM_005275010.1:c.1593+2861dup
VPS52 transcript variant X2 XM_005275011.1:c.1593+2861= XM_005275011.1:c.1593+2858_1593+2861del XM_005275011.1:c.1593+2861del XM_005275011.1:c.1593+2861dup
VPS52 transcript variant X3 XM_005275012.1:c.1419+2861= XM_005275012.1:c.1419+2858_1419+2861del XM_005275012.1:c.1419+2861del XM_005275012.1:c.1419+2861dup
VPS52 transcript variant X4 XM_005275013.1:c.1227+2861= XM_005275013.1:c.1227+2858_1227+2861del XM_005275013.1:c.1227+2861del XM_005275013.1:c.1227+2861dup
VPS52 transcript variant X1 XM_005275279.1:c.1593+2882= XM_005275279.1:c.1593+2879_1593+2882del XM_005275279.1:c.1593+2882del XM_005275279.1:c.1593+2882dup
VPS52 transcript variant X2 XM_005275280.1:c.1593+2882= XM_005275280.1:c.1593+2879_1593+2882del XM_005275280.1:c.1593+2882del XM_005275280.1:c.1593+2882dup
VPS52 transcript variant X3 XM_005275281.1:c.1419+2882= XM_005275281.1:c.1419+2879_1419+2882del XM_005275281.1:c.1419+2882del XM_005275281.1:c.1419+2882dup
VPS52 transcript variant X4 XM_005275282.1:c.1227+2882= XM_005275282.1:c.1227+2879_1227+2882del XM_005275282.1:c.1227+2882del XM_005275282.1:c.1227+2882dup
VPS52 transcript variant X1 XM_005275441.1:c.1593+2888= XM_005275441.1:c.1593+2885_1593+2888del XM_005275441.1:c.1593+2888del XM_005275441.1:c.1593+2888dup
VPS52 transcript variant X2 XM_005275442.1:c.1593+2888= XM_005275442.1:c.1593+2885_1593+2888del XM_005275442.1:c.1593+2888del XM_005275442.1:c.1593+2888dup
VPS52 transcript variant X3 XM_005275443.1:c.1419+2888= XM_005275443.1:c.1419+2885_1419+2888del XM_005275443.1:c.1419+2888del XM_005275443.1:c.1419+2888dup
VPS52 transcript variant X4 XM_005275444.1:c.1227+2888= XM_005275444.1:c.1227+2885_1227+2888del XM_005275444.1:c.1227+2888del XM_005275444.1:c.1227+2888dup
VPS52 transcript variant X1 XM_005275580.1:c.1593+2880= XM_005275580.1:c.1593+2877_1593+2880del XM_005275580.1:c.1593+2880del XM_005275580.1:c.1593+2880dup
VPS52 transcript variant X2 XM_005275581.1:c.1593+2880= XM_005275581.1:c.1593+2877_1593+2880del XM_005275581.1:c.1593+2880del XM_005275581.1:c.1593+2880dup
VPS52 transcript variant X3 XM_005275582.1:c.1419+2880= XM_005275582.1:c.1419+2877_1419+2880del XM_005275582.1:c.1419+2880del XM_005275582.1:c.1419+2880dup
VPS52 transcript variant X4 XM_005275583.1:c.1227+2880= XM_005275583.1:c.1227+2877_1227+2880del XM_005275583.1:c.1227+2880del XM_005275583.1:c.1227+2880dup
VPS52 transcript variant X3 XM_011514797.2:c.1593+2860= XM_011514797.2:c.1593+2857_1593+2860del XM_011514797.2:c.1593+2860del XM_011514797.2:c.1593+2860dup
VPS52 transcript variant X1 XM_011514798.3:c.1593+2860= XM_011514798.3:c.1593+2857_1593+2860del XM_011514798.3:c.1593+2860del XM_011514798.3:c.1593+2860dup
VPS52 transcript variant X2 XM_011514799.2:c.1593+2860= XM_011514799.2:c.1593+2857_1593+2860del XM_011514799.2:c.1593+2860del XM_011514799.2:c.1593+2860dup
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#.

4 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss4139562402 Apr 26, 2021 (155)
2 TOPMED ss4698702320 Apr 26, 2021 (155)
3 TOPMED ss4698702321 Apr 26, 2021 (155)
4 EVA ss5883297022 Oct 17, 2022 (156)
5 gnomAD - Genomes NC_000006.12 - 33260624 Apr 26, 2021 (155)
6 TopMed

Submission ignored due to conflicting rows:
Row 536079878 (NC_000006.12:33260623::T 3/264690)
Row 536079879 (NC_000006.12:33260623:TTTT: 4/264690)

- Apr 26, 2021 (155)
7 TopMed

Submission ignored due to conflicting rows:
Row 536079878 (NC_000006.12:33260623::T 3/264690)
Row 536079879 (NC_000006.12:33260623:TTTT: 4/264690)

- Apr 26, 2021 (155)
8 ALFA NC_000006.12 - 33260624 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
221539879, ss4139562402, ss4698702321 NC_000006.12:33260623:TTTT: NC_000006.12:33260623:TTTTTTT:TTT (self)
7213634713 NC_000006.12:33260623:TTTTTTT:TTT NC_000006.12:33260623:TTTTTTT:TTT (self)
ss5883297022 NC_000006.12:33260623:T: NC_000006.12:33260623:TTTTTTT:TTTT…

NC_000006.12:33260623:TTTTTTT:TTTTTT

ss4698702320 NC_000006.12:33260623::T NC_000006.12:33260623:TTTTTTT:TTTT…

NC_000006.12:33260623:TTTTTTT:TTTTTTTT

(self)
7213634713 NC_000006.12:33260623:TTTTTTT:TTTT…

NC_000006.12:33260623:TTTTTTT:TTTTTTTT

NC_000006.12:33260623:TTTTTTT:TTTT…

NC_000006.12:33260623: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 rs1491330382

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