Name: rs161315
Published: September 21, 2022
License: Open Access

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 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:149076319 (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: G>A / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.434251 (114942/264690, TOPMED)
G=0.38072 (10750/28236, 14KJPN)
T=0.4419 (4111/9304, ALFA) (+ 1 more)
G=0.4087 (2617/6404, 1000G_30x)

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: 20230706150541

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

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	G=0.434251	T=0.565749
14KJPN	JAPANESE	Study-wide	28236	G=0.38072	T=0.61928
Allele Frequency Aggregator	Total	Global	9304	G=0.5581	A=0.0000, T=0.4419
Allele Frequency Aggregator	European	Sub	8494	G=0.5253	A=0.0000, T=0.4747
Allele Frequency Aggregator	African	Sub	496	G=0.895	A=0.000, T=0.105
Allele Frequency Aggregator	Other	Sub	124	G=0.831	A=0.000, T=0.169
Allele Frequency Aggregator	Latin American 2	Sub	108	G=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	36	G=1.00	A=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	28	G=0.89	A=0.00, T=0.11
Allele Frequency Aggregator	Asian	Sub	18	G=0.83	A=0.00, T=0.17
1000Genomes_30x	Global	Study-wide	6404	G=0.4087	T=0.5913
1000Genomes_30x	African	Sub	1786	G=0.3544	T=0.6456
1000Genomes_30x	Europe	Sub	1266	G=0.4929	T=0.5071
1000Genomes_30x	South Asian	Sub	1202	G=0.3993	T=0.6007
1000Genomes_30x	East Asian	Sub	1170	G=0.3726	T=0.6274
1000Genomes_30x	American	Sub	980	G=0.453	T=0.547

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.149076319G>A
GRCh38.p14 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
NBPF9 transcript variant X1	XM_047420572.1:c.779-455C… XM_047420572.1:c.779-455C>T	N/A	Intron Variant
NBPF9 transcript variant X3	XM_047420578.1:c.779-455C… XM_047420578.1:c.779-455C>T	N/A	Intron Variant
NBPF9 transcript variant X2	XR_007060075.1:n.	N/A	Intron Variant

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

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.p14 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
NBPF9 transcript variant X1	XM_047420572.1:c.779-455=	XM_047420572.1:c.779-455C>T	XM_047420572.1:c.779-455C>A
NBPF9 transcript variant X3	XM_047420578.1:c.779-455=	XM_047420578.1:c.779-455C>T	XM_047420578.1:c.779-455C>A

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#.

36 SubSNP, 6 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	URBANLAB	ss3646784159	Oct 11, 2018 (152)
19	EVA	ss3746751498	Jul 12, 2019 (153)
20	EVA	ss3836592788	Apr 25, 2020 (154)
21	SGDP_PRJ	ss3849851343	Apr 25, 2020 (154)
22	KRGDB	ss3895021257	Apr 25, 2020 (154)
23	GNOMAD	ss4003001731	Apr 27, 2021 (155)
24	GNOMAD	ss4003001732	Apr 27, 2021 (155)
25	TOPMED	ss4467063786	Apr 27, 2021 (155)
26	TOMMO_GENOMICS	ss5146134172	Apr 27, 2021 (155)
27	1000G_HIGH_COVERAGE	ss5244166638	Oct 17, 2022 (156)
28	EVA	ss5321665084	Oct 17, 2022 (156)
29	HUGCELL_USP	ss5444787671	Oct 17, 2022 (156)
30	HUGCELL_USP	ss5444787672	Oct 17, 2022 (156)
31	1000G_HIGH_COVERAGE	ss5517432864	Oct 17, 2022 (156)
32	SANFORD_IMAGENETICS	ss5626473688	Oct 17, 2022 (156)
33	TOMMO_GENOMICS	ss5673438021	Oct 17, 2022 (156)
34	YY_MCH	ss5801230620	Oct 17, 2022 (156)
35	EVA	ss5832585458	Oct 17, 2022 (156)
36	EVA	ss5938294678	Oct 17, 2022 (156)
37	1000Genomes_30x	NC_000001.11 - 149076319	Oct 17, 2022 (156)
38	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)
39	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)
40	14KJPN	NC_000001.11 - 149076319	Oct 17, 2022 (156)
41	TopMed	NC_000001.11 - 149076319	Apr 27, 2021 (155)
42	ALFA	NC_000001.11 - 149076319	Apr 27, 2021 (155)

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, ss4003001731, ss5444787672	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, ss5321665084, ss5626473688, ss5832585458, ss5938294678	NC_000001.10:144811292:A:A	NC_000001.11:149076318:G:T	(self)
4958799, 7275125, 30670121, 8106493915, ss3646784159, ss4003001732, ss4467063786, ss5244166638, ss5444787671, ss5517432864, ss5673438021, ss5801230620	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)

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

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs161315