Name: rs5745117
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.

rs5745117

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:173149024 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.007802 (2065/264690, TOPMED)
T=0.010487 (1470/140170, GnomAD)
T=0.01569 (301/19190, ALFA) (+ 12 more)
T=0.0028 (18/6404, 1000G_30x)
T=0.0030 (15/5008, 1000G)
T=0.0328 (147/4480, Estonian)
T=0.0119 (46/3854, ALSPAC)
T=0.0156 (58/3708, TWINSUK)
T=0.0000 (0/2922, KOREAN)
T=0.012 (12/998, GoNL)
T=0.005 (3/600, NorthernSweden)
T=0.000 (0/330, HapMap)
T=0.03 (1/40, GENOME_DK)
G=0.5 (1/2, SGDP_PRJ)
T=0.5 (1/2, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: BNIP1 : 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	19190	G=0.98431	T=0.01569
European	Sub	14286	G=0.98061	T=0.01939
African	Sub	2970	G=0.9980	T=0.0020
African Others	Sub	114	G=1.000	T=0.000
African American	Sub	2856	G=0.9979	T=0.0021
Asian	Sub	116	G=1.000	T=0.000
East Asian	Sub	88	G=1.00	T=0.00
Other Asian	Sub	28	G=1.00	T=0.00
Latin American 1	Sub	154	G=0.994	T=0.006
Latin American 2	Sub	616	G=0.994	T=0.006
South Asian	Sub	98	G=1.00	T=0.00
Other	Sub	950	G=0.986	T=0.014

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=0.992198	T=0.007802
gnomAD - Genomes	Global	Study-wide	140170	G=0.989513	T=0.010487
gnomAD - Genomes	European	Sub	75902	G=0.98341	T=0.01659
gnomAD - Genomes	African	Sub	42014	G=0.99726	T=0.00274
gnomAD - Genomes	American	Sub	13648	G=0.99480	T=0.00520
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=0.9958	T=0.0042
gnomAD - Genomes	East Asian	Sub	3130	G=1.0000	T=0.0000
gnomAD - Genomes	Other	Sub	2152	G=0.9949	T=0.0051
Allele Frequency Aggregator	Total	Global	19190	G=0.98431	T=0.01569
Allele Frequency Aggregator	European	Sub	14286	G=0.98061	T=0.01939
Allele Frequency Aggregator	African	Sub	2970	G=0.9980	T=0.0020
Allele Frequency Aggregator	Other	Sub	950	G=0.986	T=0.014
Allele Frequency Aggregator	Latin American 2	Sub	616	G=0.994	T=0.006
Allele Frequency Aggregator	Latin American 1	Sub	154	G=0.994	T=0.006
Allele Frequency Aggregator	Asian	Sub	116	G=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	G=1.00	T=0.00
1000Genomes_30x	Global	Study-wide	6404	G=0.9972	T=0.0028
1000Genomes_30x	African	Sub	1786	G=0.9994	T=0.0006
1000Genomes_30x	Europe	Sub	1266	G=0.9905	T=0.0095
1000Genomes_30x	South Asian	Sub	1202	G=0.9992	T=0.0008
1000Genomes_30x	East Asian	Sub	1170	G=1.0000	T=0.0000
1000Genomes_30x	American	Sub	980	G=0.996	T=0.004
1000Genomes	Global	Study-wide	5008	G=0.9970	T=0.0030
1000Genomes	African	Sub	1322	G=0.9992	T=0.0008
1000Genomes	East Asian	Sub	1008	G=1.0000	T=0.0000
1000Genomes	Europe	Sub	1006	G=0.9901	T=0.0099
1000Genomes	South Asian	Sub	978	G=0.999	T=0.001
1000Genomes	American	Sub	694	G=0.996	T=0.004
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.9672	T=0.0328
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9881	T=0.0119
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9844	T=0.0156
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=1.0000	T=0.0000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.988	T=0.012
Northern Sweden	ACPOP	Study-wide	600	G=0.995	T=0.005
HapMap	Global	Study-wide	330	G=1.000	T=0.000
HapMap	African	Sub	120	G=1.000	T=0.000
HapMap	American	Sub	120	G=1.000	T=0.000
HapMap	Asian	Sub	90	G=1.00	T=0.00
The Danish reference pan genome	Danish	Study-wide	40	G=0.97	T=0.03
SGDP_PRJ	Global	Study-wide	2	G=0.5	T=0.5

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 5	NC_000005.10:g.173149024G>T
GRCh37.p13 chr 5	NC_000005.9:g.172576027G>T

Gene: BNIP1, BCL2 interacting protein 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
BNIP1 transcript variant BNIP1	NM_001205.3:c.177+2066G>T	N/A	Intron Variant
BNIP1 transcript variant BNIP1-a	NM_013978.3:c.177+2066G>T	N/A	Intron Variant
BNIP1 transcript variant BNIP1-b	NM_013979.3:c.177+2066G>T	N/A	Intron Variant
BNIP1 transcript variant BNIP1-c	NM_013980.3:c.177+2066G>T	N/A	Intron Variant
BNIP1 transcript variant X1	XM_011534638.2:c.177+2066… XM_011534638.2:c.177+2066G>T	N/A	Intron Variant
BNIP1 transcript variant X2	XM_011534639.2:c.177+2066… XM_011534639.2:c.177+2066G>T	N/A	Intron Variant
BNIP1 transcript variant X3	XM_047417623.1:c.177+2066… XM_047417623.1:c.177+2066G>T	N/A	Intron Variant
BNIP1 transcript variant X4	XM_047417624.1:c.177+2066… XM_047417624.1:c.177+2066G>T	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=	T
GRCh38.p14 chr 5	NC_000005.10:g.173149024=	NC_000005.10:g.173149024G>T
GRCh37.p13 chr 5	NC_000005.9:g.172576027=	NC_000005.9:g.172576027G>T
BNIP1 transcript variant BNIP1	NM_001205.2:c.177+2066=	NM_001205.2:c.177+2066G>T
BNIP1 transcript variant BNIP1	NM_001205.3:c.177+2066=	NM_001205.3:c.177+2066G>T
BNIP1 transcript variant BNIP1-a	NM_013978.2:c.177+2066=	NM_013978.2:c.177+2066G>T
BNIP1 transcript variant BNIP1-a	NM_013978.3:c.177+2066=	NM_013978.3:c.177+2066G>T
BNIP1 transcript variant BNIP1-b	NM_013979.2:c.177+2066=	NM_013979.2:c.177+2066G>T
BNIP1 transcript variant BNIP1-b	NM_013979.3:c.177+2066=	NM_013979.3:c.177+2066G>T
BNIP1 transcript variant BNIP1-c	NM_013980.2:c.177+2066=	NM_013980.2:c.177+2066G>T
BNIP1 transcript variant BNIP1-c	NM_013980.3:c.177+2066=	NM_013980.3:c.177+2066G>T
BNIP1 transcript variant X1	XM_011534638.2:c.177+2066=	XM_011534638.2:c.177+2066G>T
BNIP1 transcript variant X2	XM_011534639.2:c.177+2066=	XM_011534639.2:c.177+2066G>T
BNIP1 transcript variant X3	XM_047417623.1:c.177+2066=	XM_047417623.1:c.177+2066G>T
BNIP1 transcript variant X4	XM_047417624.1:c.177+2066=	XM_047417624.1:c.177+2066G>T

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#.

31 SubSNP, 14 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	EGP_SNPS	ss7989436	Apr 21, 2003 (114)
2	BCMHGSC_JDW	ss93338837	Mar 24, 2008 (129)
3	ENSEMBL	ss143628715	Dec 01, 2009 (131)
4	1000GENOMES	ss332985589	May 09, 2011 (134)
5	ILLUMINA	ss535257593	Sep 08, 2015 (146)
6	EVA-GONL	ss982427644	Aug 21, 2014 (142)
7	1000GENOMES	ss1318387818	Aug 21, 2014 (142)
8	EVA_GENOME_DK	ss1581468383	Apr 01, 2015 (144)
9	EVA_DECODE	ss1591970874	Apr 01, 2015 (144)
10	EVA_UK10K_ALSPAC	ss1614644231	Apr 01, 2015 (144)
11	EVA_UK10K_TWINSUK	ss1657638264	Apr 01, 2015 (144)
12	HUMAN_LONGEVITY	ss2280623693	Dec 20, 2016 (150)
13	GNOMAD	ss2834123923	Nov 08, 2017 (151)
14	SWEGEN	ss2998262352	Nov 08, 2017 (151)
15	CSHL	ss3346758901	Nov 08, 2017 (151)
16	ILLUMINA	ss3629407480	Oct 12, 2018 (152)
17	EGCUT_WGS	ss3666200645	Jul 13, 2019 (153)
18	EVA_DECODE	ss3716279506	Jul 13, 2019 (153)
19	ACPOP	ss3733068064	Jul 13, 2019 (153)
20	EVA	ss3829650235	Apr 26, 2020 (154)
21	SGDP_PRJ	ss3863584974	Apr 26, 2020 (154)
22	KRGDB	ss3910298741	Apr 26, 2020 (154)
23	TOPMED	ss4688921630	Apr 26, 2021 (155)
24	1000G_HIGH_COVERAGE	ss5266869415	Oct 13, 2022 (156)
25	EVA	ss5362862931	Oct 13, 2022 (156)
26	HUGCELL_USP	ss5464732912	Oct 13, 2022 (156)
27	1000G_HIGH_COVERAGE	ss5552050830	Oct 13, 2022 (156)
28	SANFORD_IMAGENETICS	ss5639462347	Oct 13, 2022 (156)
29	EVA	ss5836042507	Oct 13, 2022 (156)
30	EVA	ss5897516492	Oct 13, 2022 (156)
31	EVA	ss5967962257	Oct 13, 2022 (156)
32	1000Genomes	NC_000005.9 - 172576027	Oct 12, 2018 (152)
33	1000Genomes_30x	NC_000005.10 - 173149024	Oct 13, 2022 (156)
34	The Avon Longitudinal Study of Parents and Children	NC_000005.9 - 172576027	Oct 12, 2018 (152)
35	Genetic variation in the Estonian population	NC_000005.9 - 172576027	Oct 12, 2018 (152)
36	The Danish reference pan genome	NC_000005.9 - 172576027	Apr 26, 2020 (154)
37	gnomAD - Genomes	NC_000005.10 - 173149024	Apr 26, 2021 (155)
38	Genome of the Netherlands Release 5	NC_000005.9 - 172576027	Apr 26, 2020 (154)
39	HapMap	NC_000005.10 - 173149024	Apr 26, 2020 (154)
40	KOREAN population from KRGDB	NC_000005.9 - 172576027	Apr 26, 2020 (154)
41	Northern Sweden	NC_000005.9 - 172576027	Jul 13, 2019 (153)
42	SGDP_PRJ	NC_000005.9 - 172576027	Apr 26, 2020 (154)
43	TopMed	NC_000005.10 - 173149024	Apr 26, 2021 (155)
44	UK 10K study - Twins	NC_000005.9 - 172576027	Oct 12, 2018 (152)
45	ALFA	NC_000005.10 - 173149024	Apr 26, 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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss93338837, ss1591970874	NC_000005.8:172508632:G:T	NC_000005.10:173149023:G:T	(self)
30108037, 16763520, 11938893, 7633322, 7439497, 17476135, 6352929, 15601954, 16763520, ss332985589, ss535257593, ss982427644, ss1318387818, ss1581468383, ss1614644231, ss1657638264, ss2834123923, ss2998262352, ss3346758901, ss3629407480, ss3666200645, ss3733068064, ss3829650235, ss3863584974, ss3910298741, ss5362862931, ss5639462347, ss5836042507, ss5967962257	NC_000005.9:172576026:G:T	NC_000005.10:173149023:G:T	(self)
39576765, 212942676, 3029307, 526299187, 6499753972, ss2280623693, ss3716279506, ss4688921630, ss5266869415, ss5464732912, ss5552050830, ss5897516492	NC_000005.10:173149023:G:T	NC_000005.10:173149023:G:T	(self)
ss7989436, ss143628715	NT_023133.13:17387299:G:T	NC_000005.10:173149023: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 rs5745117

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs5745117