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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.

rs782072027

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:149075731 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000004 (1/264690, TOPMED)
T=0.000009 (1/115174, ExAC)
T=0.00000 (0/11862, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NBPF9 : Synonymous 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 C=1.00000 T=0.00000 1.0 0.0 0.0 N/A
European Sub 7618 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Sub 2816 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Others Sub 108 C=1.000 T=0.000 1.0 0.0 0.0 N/A
African American Sub 2708 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 146 C=1.000 T=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 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 470 C=1.000 T=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
TopMed Global Study-wide 264690 C=0.999996 T=0.000004
ExAC Global Study-wide 115174 C=0.999991 T=0.000009
ExAC Europe Sub 69768 C=1.00000 T=0.00000
ExAC Asian Sub 24516 C=1.00000 T=0.00000
ExAC American Sub 11428 C=0.99991 T=0.00009
ExAC African Sub 8578 C=1.0000 T=0.0000
ExAC Other Sub 884 C=1.000 T=0.000
Allele Frequency Aggregator Total Global 11862 C=1.00000 T=0.00000
Allele Frequency Aggregator European Sub 7618 C=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 2816 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 T=0.000
Allele Frequency Aggregator Other Sub 470 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 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 1 NC_000001.11:g.149075731C>T
GRCh37.p13 chr 1 fix patch HG1287_PATCH NW_003871055.3:g.5891144C>T
GRCh37.p13 chr 1 NC_000001.10:g.144811881G>A
Gene: NBPF9, NBPF member 9 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
NBPF9 transcript variant 13 NM_001388376.1:c.912G>A Q [CAG] > Q [CAA] Coding Sequence Variant
NBPF family member NBPF9 isoform 2 NP_001375305.1:p.Gln304= Q (Gln) > Q (Gln) Synonymous Variant
NBPF9 transcript variant 2 NM_001037675.4:c.912G>A Q [CAG] > Q [CAA] Coding Sequence Variant
NBPF family member NBPF9 isoform 2 NP_001032764.2:p.Gln304= Q (Gln) > Q (Gln) Synonymous Variant
NBPF9 transcript variant 10 NM_001388373.1:c.912G>A Q [CAG] > Q [CAA] Coding Sequence Variant
NBPF family member NBPF9 isoform 2 NP_001375302.1:p.Gln304= Q (Gln) > Q (Gln) Synonymous Variant
NBPF9 transcript variant 16 NM_001388379.1:c.912G>A Q [CAG] > Q [CAA] Coding Sequence Variant
NBPF family member NBPF9 isoform 2 NP_001375308.1:p.Gln304= Q (Gln) > Q (Gln) Synonymous Variant
NBPF9 transcript variant 6 NM_001388369.1:c.912G>A Q [CAG] > Q [CAA] Coding Sequence Variant
NBPF family member NBPF9 isoform 1 NP_001375298.1:p.Gln304= Q (Gln) > Q (Gln) Synonymous Variant
NBPF9 transcript variant 9 NM_001388372.1:c.912G>A Q [CAG] > Q [CAA] Coding Sequence Variant
NBPF family member NBPF9 isoform 2 NP_001375301.1:p.Gln304= Q (Gln) > Q (Gln) Synonymous Variant
NBPF9 transcript variant 1 NM_001277444.2:c.912G>A Q [CAG] > Q [CAA] Coding Sequence Variant
NBPF family member NBPF9 isoform 1 NP_001264373.1:p.Gln304= Q (Gln) > Q (Gln) Synonymous Variant
NBPF9 transcript variant 4 NM_001388367.1:c.912G>A Q [CAG] > Q [CAA] Coding Sequence Variant
NBPF family member NBPF9 isoform 1 NP_001375296.1:p.Gln304= Q (Gln) > Q (Gln) Synonymous Variant
NBPF9 transcript variant 5 NM_001388368.1:c.912G>A Q [CAG] > Q [CAA] Coding Sequence Variant
NBPF family member NBPF9 isoform 1 NP_001375297.1:p.Gln304= Q (Gln) > Q (Gln) Synonymous Variant
NBPF9 transcript variant 11 NM_001388374.1:c.912G>A Q [CAG] > Q [CAA] Coding Sequence Variant
NBPF family member NBPF9 isoform 2 NP_001375303.1:p.Gln304= Q (Gln) > Q (Gln) Synonymous Variant
NBPF9 transcript variant 8 NM_001388371.1:c.912G>A Q [CAG] > Q [CAA] Coding Sequence Variant
NBPF family member NBPF9 isoform 3 NP_001375300.1:p.Gln304= Q (Gln) > Q (Gln) Synonymous Variant
NBPF9 transcript variant 17 NM_001388381.1:c.912G>A Q [CAG] > Q [CAA] Coding Sequence Variant
NBPF family member NBPF9 isoform 2 NP_001375310.1:p.Gln304= Q (Gln) > Q (Gln) Synonymous Variant
NBPF9 transcript variant 14 NM_001388377.1:c.912G>A Q [CAG] > Q [CAA] Coding Sequence Variant
NBPF family member NBPF9 isoform 2 NP_001375306.1:p.Gln304= Q (Gln) > Q (Gln) Synonymous Variant
NBPF9 transcript variant 3 NM_001388366.1:c.912G>A Q [CAG] > Q [CAA] Coding Sequence Variant
NBPF family member NBPF9 isoform 1 NP_001375295.1:p.Gln304= Q (Gln) > Q (Gln) Synonymous Variant
NBPF9 transcript variant 18 NM_001388382.1:c.912G>A Q [CAG] > Q [CAA] Coding Sequence Variant
NBPF family member NBPF9 isoform 2 NP_001375311.1:p.Gln304= Q (Gln) > Q (Gln) Synonymous Variant
NBPF9 transcript variant 20 NM_001388384.1:c.912G>A Q [CAG] > Q [CAA] Coding Sequence Variant
NBPF family member NBPF9 isoform 2 NP_001375313.1:p.Gln304= Q (Gln) > Q (Gln) Synonymous Variant
NBPF9 transcript variant 7 NM_001388370.1:c.912G>A Q [CAG] > Q [CAA] Coding Sequence Variant
NBPF family member NBPF9 isoform 1 NP_001375299.1:p.Gln304= Q (Gln) > Q (Gln) Synonymous Variant
NBPF9 transcript variant 15 NM_001388378.1:c.912G>A Q [CAG] > Q [CAA] Coding Sequence Variant
NBPF family member NBPF9 isoform 2 NP_001375307.1:p.Gln304= Q (Gln) > Q (Gln) Synonymous Variant
NBPF9 transcript variant 19 NM_001388383.1:c.912G>A Q [CAG] > Q [CAA] Coding Sequence Variant
NBPF family member NBPF9 isoform 2 NP_001375312.1:p.Gln304= Q (Gln) > Q (Gln) Synonymous Variant
NBPF9 transcript variant 12 NM_001388375.1:c.912G>A Q [CAG] > Q [CAA] Coding Sequence Variant
NBPF family member NBPF9 isoform 2 NP_001375304.1:p.Gln304= Q (Gln) > Q (Gln) Synonymous Variant
NBPF9 transcript variant X1 XM_047420572.1:c.912G>A Q [CAG] > Q [CAA] Coding Sequence Variant
neuroblastoma breakpoint family member 9 isoform X1 XP_047276528.1:p.Gln304= Q (Gln) > Q (Gln) Synonymous Variant
NBPF9 transcript variant X3 XM_047420578.1:c.912G>A Q [CAG] > Q [CAA] Coding Sequence Variant
neuroblastoma breakpoint family member 9 isoform X2 XP_047276534.1:p.Gln304= Q (Gln) > Q (Gln) Synonymous Variant
NBPF9 transcript variant X2 XR_007060075.1:n.4891G>A 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 C= T
GRCh38.p14 chr 1 NC_000001.11:g.149075731= NC_000001.11:g.149075731C>T
GRCh37.p13 chr 1 fix patch HG1287_PATCH NW_003871055.3:g.5891144= NW_003871055.3:g.5891144C>T
GRCh37.p13 chr 1 NC_000001.10:g.144811881= NC_000001.10:g.144811881G>A
NBPF9 transcript variant 2 NM_001037675.4:c.912= NM_001037675.4:c.912G>A
NBPF9 transcript variant 2 NM_001037675.3:c.912= NM_001037675.3:c.912G>A
NBPF9 transcript variant 1 NM_001277444.2:c.912= NM_001277444.2:c.912G>A
NBPF9 transcript variant 1 NM_001277444.1:c.912= NM_001277444.1:c.912G>A
NBPF9 transcript variant 5 NM_001388368.1:c.912= NM_001388368.1:c.912G>A
NBPF9 transcript variant 7 NM_001388370.1:c.912= NM_001388370.1:c.912G>A
NBPF9 transcript variant 3 NM_001388366.1:c.912= NM_001388366.1:c.912G>A
NBPF9 transcript variant 6 NM_001388369.1:c.912= NM_001388369.1:c.912G>A
NBPF9 transcript variant 8 NM_001388371.1:c.912= NM_001388371.1:c.912G>A
NBPF9 transcript variant 4 NM_001388367.1:c.912= NM_001388367.1:c.912G>A
NBPF9 transcript variant 13 NM_001388376.1:c.912= NM_001388376.1:c.912G>A
NBPF9 transcript variant 15 NM_001388378.1:c.912= NM_001388378.1:c.912G>A
NBPF9 transcript variant 12 NM_001388375.1:c.912= NM_001388375.1:c.912G>A
NBPF9 transcript variant 9 NM_001388372.1:c.912= NM_001388372.1:c.912G>A
NBPF9 transcript variant 14 NM_001388377.1:c.912= NM_001388377.1:c.912G>A
NBPF9 transcript variant 20 NM_001388384.1:c.912= NM_001388384.1:c.912G>A
NBPF9 transcript variant 19 NM_001388383.1:c.912= NM_001388383.1:c.912G>A
NBPF9 transcript variant X2 XR_007060075.1:n.4891= XR_007060075.1:n.4891G>A
NBPF9 transcript variant X3 XM_047420578.1:c.912= XM_047420578.1:c.912G>A
NBPF9 transcript variant 18 NM_001388382.1:c.912= NM_001388382.1:c.912G>A
NBPF9 transcript variant 17 NM_001388381.1:c.912= NM_001388381.1:c.912G>A
NBPF9 transcript variant 11 NM_001388374.1:c.912= NM_001388374.1:c.912G>A
NBPF9 transcript variant 10 NM_001388373.1:c.912= NM_001388373.1:c.912G>A
NBPF9 transcript variant 16 NM_001388379.1:c.912= NM_001388379.1:c.912G>A
NBPF9 transcript variant X1 XM_047420572.1:c.912= XM_047420572.1:c.912G>A
NBPF family member NBPF9 isoform 2 NP_001032764.2:p.Gln304= NP_001032764.2:p.Gln304=
NBPF family member NBPF9 isoform 1 NP_001264373.1:p.Gln304= NP_001264373.1:p.Gln304=
NBPF family member NBPF9 isoform 1 NP_001375297.1:p.Gln304= NP_001375297.1:p.Gln304=
NBPF family member NBPF9 isoform 1 NP_001375299.1:p.Gln304= NP_001375299.1:p.Gln304=
NBPF family member NBPF9 isoform 1 NP_001375295.1:p.Gln304= NP_001375295.1:p.Gln304=
NBPF family member NBPF9 isoform 1 NP_001375298.1:p.Gln304= NP_001375298.1:p.Gln304=
NBPF family member NBPF9 isoform 3 NP_001375300.1:p.Gln304= NP_001375300.1:p.Gln304=
NBPF family member NBPF9 isoform 1 NP_001375296.1:p.Gln304= NP_001375296.1:p.Gln304=
NBPF family member NBPF9 isoform 2 NP_001375305.1:p.Gln304= NP_001375305.1:p.Gln304=
NBPF family member NBPF9 isoform 2 NP_001375307.1:p.Gln304= NP_001375307.1:p.Gln304=
NBPF family member NBPF9 isoform 2 NP_001375304.1:p.Gln304= NP_001375304.1:p.Gln304=
NBPF family member NBPF9 isoform 2 NP_001375301.1:p.Gln304= NP_001375301.1:p.Gln304=
NBPF family member NBPF9 isoform 2 NP_001375306.1:p.Gln304= NP_001375306.1:p.Gln304=
NBPF family member NBPF9 isoform 2 NP_001375313.1:p.Gln304= NP_001375313.1:p.Gln304=
NBPF family member NBPF9 isoform 2 NP_001375312.1:p.Gln304= NP_001375312.1:p.Gln304=
neuroblastoma breakpoint family member 9 isoform X2 XP_047276534.1:p.Gln304= XP_047276534.1:p.Gln304=
NBPF family member NBPF9 isoform 2 NP_001375311.1:p.Gln304= NP_001375311.1:p.Gln304=
NBPF family member NBPF9 isoform 2 NP_001375310.1:p.Gln304= NP_001375310.1:p.Gln304=
NBPF family member NBPF9 isoform 2 NP_001375303.1:p.Gln304= NP_001375303.1:p.Gln304=
NBPF family member NBPF9 isoform 2 NP_001375302.1:p.Gln304= NP_001375302.1:p.Gln304=
NBPF family member NBPF9 isoform 2 NP_001375308.1:p.Gln304= NP_001375308.1:p.Gln304=
neuroblastoma breakpoint family member 9 isoform X1 XP_047276528.1:p.Gln304= XP_047276528.1:p.Gln304=
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#.

5 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1685724548 Apr 09, 2015 (144)
2 GNOMAD ss2731770669 Oct 11, 2018 (152)
3 GNOMAD ss2746411622 Oct 11, 2018 (152)
4 GNOMAD ss2760535119 Oct 11, 2018 (152)
5 TOPMED ss4467063588 Apr 27, 2021 (155)
6 ExAC NC_000001.10 - 144811881 Oct 11, 2018 (152)
7 TopMed NC_000001.11 - 149075731 Apr 27, 2021 (155)
8 ALFA NC_000001.11 - 149075731 Apr 27, 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
4936432, ss1685724548, ss2731770669, ss2746411622, ss2760535119 NC_000001.10:144811880:G:A NC_000001.11:149075730:C:T (self)
30669923, 10877407628, ss4467063588 NC_000001.11:149075730:C:T NC_000001.11:149075730: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 rs782072027

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