Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs161315

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:149076319 (GRCh38.p13) 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
G>A / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.434251 (114942/264690, TOPMED)
T=0.4419 (4111/9304, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NBPF9 : 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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 9304 G=0.5581 A=0.0000, T=0.4419
European Sub 8494 G=0.5253 A=0.0000, T=0.4747
African Sub 496 G=0.895 A=0.000, T=0.105
African Others Sub 16 G=0.75 A=0.00, T=0.25
African American Sub 480 G=0.900 A=0.000, T=0.100
Asian Sub 18 G=0.83 A=0.00, T=0.17
East Asian Sub 10 G=0.8 A=0.0, T=0.2
Other Asian Sub 8 G=0.9 A=0.0, T=0.1
Latin American 1 Sub 36 G=1.00 A=0.00, T=0.00
Latin American 2 Sub 108 G=1.000 A=0.000, T=0.000
South Asian Sub 28 G=0.89 A=0.00, T=0.11
Other Sub 124 G=0.831 A=0.000, T=0.169


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 G=0.434251 T=0.565749
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.p13 chr 1 NC_000001.11:g.149076319G>A
GRCh38.p13 chr 1 NC_000001.11:g.149076319G>T
GRCh37.p13 chr 1 fix patch HG1287_PATCH NW_003871055.3:g.5891732G>A
GRCh37.p13 chr 1 fix patch HG1287_PATCH NW_003871055.3:g.5891732G>T
GRCh37.p13 chr 1 NC_000001.10:g.144811293A>C
GRCh37.p13 chr 1 NC_000001.10:g.144811293A>T
Gene: NBPF9, NBPF member 9 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
NBPF9 transcript variant 2 NM_001037675.4:c.779-455C…

NM_001037675.4:c.779-455C>T

N/A Intron Variant
NBPF9 transcript variant 1 NM_001277444.2:c.779-455C…

NM_001277444.2:c.779-455C>T

N/A Intron Variant
NBPF9 transcript variant 3 NM_001388366.1:c.779-455C…

NM_001388366.1:c.779-455C>T

N/A Intron Variant
NBPF9 transcript variant 4 NM_001388367.1:c.779-455C…

NM_001388367.1:c.779-455C>T

N/A Intron Variant
NBPF9 transcript variant 5 NM_001388368.1:c.779-455C…

NM_001388368.1:c.779-455C>T

N/A Intron Variant
NBPF9 transcript variant 6 NM_001388369.1:c.779-455C…

NM_001388369.1:c.779-455C>T

N/A Intron Variant
NBPF9 transcript variant 7 NM_001388370.1:c.779-455C…

NM_001388370.1:c.779-455C>T

N/A Intron Variant
NBPF9 transcript variant 8 NM_001388371.1:c.779-455C…

NM_001388371.1:c.779-455C>T

N/A Intron Variant
NBPF9 transcript variant 9 NM_001388372.1:c.779-455C…

NM_001388372.1:c.779-455C>T

N/A Intron Variant
NBPF9 transcript variant 10 NM_001388373.1:c.779-455C…

NM_001388373.1:c.779-455C>T

N/A Intron Variant
NBPF9 transcript variant 11 NM_001388374.1:c.779-455C…

NM_001388374.1:c.779-455C>T

N/A Intron Variant
NBPF9 transcript variant 12 NM_001388375.1:c.779-455C…

NM_001388375.1:c.779-455C>T

N/A Intron Variant
NBPF9 transcript variant 13 NM_001388376.1:c.779-455C…

NM_001388376.1:c.779-455C>T

N/A Intron Variant
NBPF9 transcript variant 14 NM_001388377.1:c.779-455C…

NM_001388377.1:c.779-455C>T

N/A Intron Variant
NBPF9 transcript variant 15 NM_001388378.1:c.779-455C…

NM_001388378.1:c.779-455C>T

N/A Intron Variant
NBPF9 transcript variant 16 NM_001388379.1:c.779-455C…

NM_001388379.1:c.779-455C>T

N/A Intron Variant
NBPF9 transcript variant 17 NM_001388381.1:c.779-455C…

NM_001388381.1:c.779-455C>T

N/A Intron Variant
NBPF9 transcript variant 18 NM_001388382.1:c.779-455C…

NM_001388382.1:c.779-455C>T

N/A Intron Variant
NBPF9 transcript variant 19 NM_001388383.1:c.779-455C…

NM_001388383.1:c.779-455C>T

N/A Intron Variant
NBPF9 transcript variant 20 NM_001388384.1:c.779-455C…

NM_001388384.1:c.779-455C>T

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 G= A T
GRCh38.p13 chr 1 NC_000001.11:g.149076319= NC_000001.11:g.149076319G>A NC_000001.11:g.149076319G>T
GRCh37.p13 chr 1 fix patch HG1287_PATCH NW_003871055.3:g.5891732= NW_003871055.3:g.5891732G>A NW_003871055.3:g.5891732G>T
GRCh37.p13 chr 1 NC_000001.10:g.144811293A>C NC_000001.10:g.144811293A>T NC_000001.10:g.144811293=
NBPF9 transcript variant 2 NM_001037675.3:c.779-455= NM_001037675.3:c.779-455C>T NM_001037675.3:c.779-455C>A
NBPF9 transcript variant 2 NM_001037675.4:c.779-455= NM_001037675.4:c.779-455C>T NM_001037675.4:c.779-455C>A
NBPF9 transcript variant 1 NM_001277444.1:c.779-455= NM_001277444.1:c.779-455C>T NM_001277444.1:c.779-455C>A
NBPF9 transcript variant 1 NM_001277444.2:c.779-455= NM_001277444.2:c.779-455C>T NM_001277444.2:c.779-455C>A
NBPF9 transcript variant 3 NM_001388366.1:c.779-455= NM_001388366.1:c.779-455C>T NM_001388366.1:c.779-455C>A
NBPF9 transcript variant 4 NM_001388367.1:c.779-455= NM_001388367.1:c.779-455C>T NM_001388367.1:c.779-455C>A
NBPF9 transcript variant 5 NM_001388368.1:c.779-455= NM_001388368.1:c.779-455C>T NM_001388368.1:c.779-455C>A
NBPF9 transcript variant 6 NM_001388369.1:c.779-455= NM_001388369.1:c.779-455C>T NM_001388369.1:c.779-455C>A
NBPF9 transcript variant 7 NM_001388370.1:c.779-455= NM_001388370.1:c.779-455C>T NM_001388370.1:c.779-455C>A
NBPF9 transcript variant 8 NM_001388371.1:c.779-455= NM_001388371.1:c.779-455C>T NM_001388371.1:c.779-455C>A
NBPF9 transcript variant 9 NM_001388372.1:c.779-455= NM_001388372.1:c.779-455C>T NM_001388372.1:c.779-455C>A
NBPF9 transcript variant 10 NM_001388373.1:c.779-455= NM_001388373.1:c.779-455C>T NM_001388373.1:c.779-455C>A
NBPF9 transcript variant 11 NM_001388374.1:c.779-455= NM_001388374.1:c.779-455C>T NM_001388374.1:c.779-455C>A
NBPF9 transcript variant 12 NM_001388375.1:c.779-455= NM_001388375.1:c.779-455C>T NM_001388375.1:c.779-455C>A
NBPF9 transcript variant 13 NM_001388376.1:c.779-455= NM_001388376.1:c.779-455C>T NM_001388376.1:c.779-455C>A
NBPF9 transcript variant 14 NM_001388377.1:c.779-455= NM_001388377.1:c.779-455C>T NM_001388377.1:c.779-455C>A
NBPF9 transcript variant 15 NM_001388378.1:c.779-455= NM_001388378.1:c.779-455C>T NM_001388378.1:c.779-455C>A
NBPF9 transcript variant 16 NM_001388379.1:c.779-455= NM_001388379.1:c.779-455C>T NM_001388379.1:c.779-455C>A
NBPF9 transcript variant 17 NM_001388381.1:c.779-455= NM_001388381.1:c.779-455C>T NM_001388381.1:c.779-455C>A
NBPF9 transcript variant 18 NM_001388382.1:c.779-455= NM_001388382.1:c.779-455C>T NM_001388382.1:c.779-455C>A
NBPF9 transcript variant 19 NM_001388383.1:c.779-455= NM_001388383.1:c.779-455C>T NM_001388383.1:c.779-455C>A
NBPF9 transcript variant 20 NM_001388384.1:c.779-455= NM_001388384.1:c.779-455C>T NM_001388384.1:c.779-455C>A
NBPF9 transcript variant X1 XM_005277393.1:c.779-455= XM_005277393.1:c.779-455C>T XM_005277393.1:c.779-455C>A
NBPF9 transcript variant X2 XM_005277394.1:c.554-455= XM_005277394.1:c.554-455C>T XM_005277394.1:c.554-455C>A
NBPF9 transcript variant X3 XM_005277395.1:c.554-455= XM_005277395.1:c.554-455C>T XM_005277395.1:c.554-455C>A
NBPF9 transcript variant X4 XM_005277396.1:c.-405-455= XM_005277396.1:c.-405-455C>T XM_005277396.1:c.-405-455C>A
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#.

28 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss783431 Aug 11, 2000 (87)
2 TSC-CSHL ss3061302 Jun 15, 2001 (106)
3 WI_SSAHASNP ss6398550 Feb 20, 2003 (111)
4 BCM_SSAHASNP ss9809580 Jul 11, 2003 (116)
5 SSAHASNP ss35307303 May 24, 2005 (146)
6 ENSEMBL ss139750144 Dec 01, 2009 (146)
7 1000GENOMES ss328912223 May 09, 2011 (146)
8 SSMP ss648375614 Apr 25, 2013 (146)
9 EVA-GONL ss975637153 Apr 09, 2015 (144)
10 1000GENOMES ss1292718301 Aug 28, 2014 (146)
11 DDI ss1425960930 Apr 09, 2015 (144)
12 WEILL_CORNELL_DGM ss1918853623 Feb 17, 2016 (147)
13 JJLAB ss2019948173 Sep 28, 2016 (149)
14 USC_VALOUEV ss2147969121 Oct 11, 2018 (152)
15 GRF ss2697926847 Oct 11, 2018 (152)
16 GNOMAD ss2760535016 Oct 11, 2018 (152)
17 SWEGEN ss2987623764 Oct 11, 2018 (152)
18 TOPMED ss3091148195 Nov 08, 2017 (151)
19 TOPMED ss3091148196 Nov 08, 2017 (151)
20 URBANLAB ss3646784159 Oct 11, 2018 (152)
21 EVA ss3746751498 Jul 12, 2019 (153)
22 EVA ss3836592788 Apr 25, 2020 (154)
23 SGDP_PRJ ss3849851343 Apr 25, 2020 (154)
24 KRGDB ss3895021257 Apr 25, 2020 (154)
25 GNOMAD ss4003001731 Apr 27, 2021 (155)
26 GNOMAD ss4003001732 Apr 27, 2021 (155)
27 TOPMED ss4467063786 Apr 27, 2021 (155)
28 TOMMO_GENOMICS ss5146134172 Apr 27, 2021 (155)
29 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 25982441 (NC_000001.11:149076318:G:A 8/138440)
Row 25982442 (NC_000001.11:149076318:G:T 78105/138314)

- Apr 27, 2021 (155)
30 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 25982441 (NC_000001.11:149076318:G:A 8/138440)
Row 25982442 (NC_000001.11:149076318:G:T 78105/138314)

- Apr 27, 2021 (155)
31 TopMed NC_000001.11 - 149076319 Apr 27, 2021 (155)
32 ALFA NC_000001.11 - 149076319 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).

Associated ID History Updated (Build)
rs611250 Oct 23, 2000 (87)
rs2135799 Jul 03, 2002 (106)
rs7537455 Aug 27, 2003 (117)
rs28552671 Sep 08, 2015 (146)
rs61805446 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss2760535016 NC_000001.10:144811292:A:T NC_000001.11:149076318:G:A (self)
8106493915, ss3091148195, ss4003001731 NC_000001.11:149076318:G:A NC_000001.11:149076318:G:A (self)
ss328912223, ss648375614, ss975637153, ss1292718301, ss1425960930, ss1918853623, ss2019948173, ss2147969121, ss2697926847, ss2760535016, ss2987623764, ss3746751498, ss3836592788, ss3849851343, ss3895021257, ss5146134172 NC_000001.10:144811292:A:A NC_000001.11:149076318:G:T (self)
19264852, 30670121, 8106493915, ss3091148196, ss3646784159, ss4003001732, ss4467063786 NC_000001.11:149076318:G:T NC_000001.11:149076318:G:T (self)
ss9809580 NT_077949.1:170800:C:A NC_000001.11:149076318:G:T (self)
ss783431, ss3061302, ss6398550, ss35307303, ss139750144 NT_167185.1:138879:A:A NC_000001.11:149076318:G: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 rs161315

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.post629+eb05767