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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.

rs772028862

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:43523823-43523824 (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
delAA
Variation Type
Deletion
Frequency
delAA=0.000008 (2/264690, TOPMED)
delAA=0.000004 (1/249234, GnomAD_exome)
delAA=0.000008 (1/120660, ExAC) (+ 1 more)
delAA=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
XPO5 : Non Coding Transcript Variant
POLR1C : 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 14050 AA=1.00000 =0.00000
European Sub 9690 AA=1.0000 =0.0000
African Sub 2898 AA=1.0000 =0.0000
African Others Sub 114 AA=1.000 =0.000
African American Sub 2784 AA=1.0000 =0.0000
Asian Sub 112 AA=1.000 =0.000
East Asian Sub 86 AA=1.00 =0.00
Other Asian Sub 26 AA=1.00 =0.00
Latin American 1 Sub 146 AA=1.000 =0.000
Latin American 2 Sub 610 AA=1.000 =0.000
South Asian Sub 98 AA=1.00 =0.00
Other Sub 496 AA=1.000 =0.000


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 AA=0.999992 delAA=0.000008
gnomAD - Exomes Global Study-wide 249234 AA=0.999996 delAA=0.000004
gnomAD - Exomes European Sub 134534 AA=0.999993 delAA=0.000007
gnomAD - Exomes Asian Sub 48576 AA=1.00000 delAA=0.00000
gnomAD - Exomes American Sub 34522 AA=1.00000 delAA=0.00000
gnomAD - Exomes African Sub 15482 AA=1.00000 delAA=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10064 AA=1.00000 delAA=0.00000
gnomAD - Exomes Other Sub 6056 AA=1.0000 delAA=0.0000
ExAC Global Study-wide 120660 AA=0.999992 delAA=0.000008
ExAC Europe Sub 73304 AA=0.99999 delAA=0.00001
ExAC Asian Sub 25126 AA=1.00000 delAA=0.00000
ExAC American Sub 11566 AA=1.00000 delAA=0.00000
ExAC African Sub 9766 AA=1.0000 delAA=0.0000
ExAC Other Sub 898 AA=1.000 delAA=0.000
Allele Frequency Aggregator Total Global 14050 AA=1.00000 delAA=0.00000
Allele Frequency Aggregator European Sub 9690 AA=1.0000 delAA=0.0000
Allele Frequency Aggregator African Sub 2898 AA=1.0000 delAA=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 AA=1.000 delAA=0.000
Allele Frequency Aggregator Other Sub 496 AA=1.000 delAA=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 AA=1.000 delAA=0.000
Allele Frequency Aggregator Asian Sub 112 AA=1.000 delAA=0.000
Allele Frequency Aggregator South Asian Sub 98 AA=1.00 delAA=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.43523823_43523824del
GRCh37.p13 chr 6 NC_000006.11:g.43491561_43491562del
POLR1C RefSeqGene NG_028283.3:g.19122_19123del
XPO5 RefSeqGene NG_051658.1:g.57252_57253del
Gene: POLR1C, RNA polymerase I and III subunit C (plus strand)
Molecule type Change Amino acid[Codon] SO Term
POLR1C transcript variant 2 NM_001318876.2:c.922+2775…

NM_001318876.2:c.922+2775_922+2776del

N/A Intron Variant
POLR1C transcript variant 3 NM_001363658.2:c.922+2775…

NM_001363658.2:c.922+2775_922+2776del

N/A Intron Variant
POLR1C transcript variant 1 NM_203290.4:c. N/A Genic Downstream Transcript Variant
POLR1C transcript variant X1 XM_047419577.1:c.922+2775…

XM_047419577.1:c.922+2775_922+2776del

N/A Intron Variant
Gene: XPO5, exportin 5 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
XPO5 transcript variant 1 NM_020750.3:c.*44_*45= N/A 3 Prime UTR Variant
XPO5 transcript variant 2 NR_144392.2:n.3971_3972del N/A Non Coding 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 AA= delAA
GRCh38.p14 chr 6 NC_000006.12:g.43523823_43523824= NC_000006.12:g.43523823_43523824del
GRCh37.p13 chr 6 NC_000006.11:g.43491561_43491562= NC_000006.11:g.43491561_43491562del
POLR1C RefSeqGene NG_028283.3:g.19122_19123= NG_028283.3:g.19122_19123del
XPO5 RefSeqGene NG_051658.1:g.57252_57253= NG_051658.1:g.57252_57253del
XPO5 transcript variant 1 NM_020750.3:c.*44_*45= NM_020750.3:c.*44_*45del
XPO5 transcript variant 1 NM_020750.2:c.*44_*45= NM_020750.2:c.*44_*45del
XPO5 transcript variant 2 NR_144392.2:n.3971_3972= NR_144392.2:n.3971_3972del
XPO5 transcript variant 2 NR_144392.1:n.4008_4009= NR_144392.1:n.4008_4009del
POLR1C transcript variant 2 NM_001318876.2:c.922+2775= NM_001318876.2:c.922+2775_922+2776del
POLR1C transcript variant 3 NM_001363658.2:c.922+2775= NM_001363658.2:c.922+2775_922+2776del
POLR1C transcript variant X1 XM_005249491.1:c.922+2775= XM_005249491.1:c.922+2775_922+2776del
POLR1C transcript variant X1 XM_047419577.1:c.922+2775= XM_047419577.1:c.922+2775_922+2776del
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#.

3 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1711825041 Apr 01, 2015 (144)
2 GNOMAD ss2735810010 Nov 08, 2017 (151)
3 TOPMED ss4701097121 Apr 26, 2021 (155)
4 ExAC NC_000006.11 - 43491561 Oct 12, 2018 (152)
5 gnomAD - Exomes NC_000006.11 - 43491561 Jul 13, 2019 (153)
6 TopMed NC_000006.12 - 43523823 Apr 26, 2021 (155)
7 ALFA NC_000006.12 - 43523823 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
8368181, 4953930, ss1711825041, ss2735810010 NC_000006.11:43491560:AA: NC_000006.12:43523822:AA: (self)
538474679, 4755866005, ss4701097121 NC_000006.12:43523822:AA: NC_000006.12:43523822:AA: (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 rs772028862

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