Name: rs116124913
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.

rs116124913

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:53934586 (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=0.014432 (3820/264690, TOPMED)
T=0.018428 (2583/140170, GnomAD)
T=0.02403 (454/18890, ALFA) (+ 11 more)
T=0.0084 (54/6404, 1000G_30x)
T=0.0098 (49/5008, 1000G)
T=0.0442 (198/4480, Estonian)
T=0.0324 (125/3854, ALSPAC)
T=0.0264 (98/3708, TWINSUK)
T=0.0003 (1/2922, KOREAN)
T=0.0005 (1/1832, Korea1K)
T=0.029 (29/998, GoNL)
T=0.050 (30/600, NorthernSweden)
T=0.03 (1/40, GENOME_DK)
C=0.44 (7/16, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: HSPB11 : 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	18890	C=0.97597	T=0.02403
European	Sub	14286	C=0.97011	T=0.02989
African	Sub	2946	C=0.9959	T=0.0041
African Others	Sub	114	C=1.000	T=0.000
African American	Sub	2832	C=0.9958	T=0.0042
Asian	Sub	112	C=1.000	T=0.000
East Asian	Sub	86	C=1.00	T=0.00
Other Asian	Sub	26	C=1.00	T=0.00
Latin American 1	Sub	146	C=1.000	T=0.000
Latin American 2	Sub	610	C=0.992	T=0.008
South Asian	Sub	98	C=1.00	T=0.00
Other	Sub	692	C=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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	C=0.985568	T=0.014432
gnomAD - Genomes	Global	Study-wide	140170	C=0.981572	T=0.018428
gnomAD - Genomes	European	Sub	75910	C=0.97120	T=0.02880
gnomAD - Genomes	African	Sub	42024	C=0.99534	T=0.00466
gnomAD - Genomes	American	Sub	13634	C=0.98841	T=0.01159
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.9952	T=0.0048
gnomAD - Genomes	East Asian	Sub	3130	C=1.0000	T=0.0000
gnomAD - Genomes	Other	Sub	2152	C=0.9875	T=0.0125
Allele Frequency Aggregator	Total	Global	18890	C=0.97597	T=0.02403
Allele Frequency Aggregator	European	Sub	14286	C=0.97011	T=0.02989
Allele Frequency Aggregator	African	Sub	2946	C=0.9959	T=0.0041
Allele Frequency Aggregator	Other	Sub	692	C=0.986	T=0.014
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.992	T=0.008
Allele Frequency Aggregator	Latin American 1	Sub	146	C=1.000	T=0.000
Allele Frequency Aggregator	Asian	Sub	112	C=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	C=1.00	T=0.00
1000Genomes_30x	Global	Study-wide	6404	C=0.9916	T=0.0084
1000Genomes_30x	African	Sub	1786	C=0.9978	T=0.0022
1000Genomes_30x	Europe	Sub	1266	C=0.9692	T=0.0308
1000Genomes_30x	South Asian	Sub	1202	C=0.9975	T=0.0025
1000Genomes_30x	East Asian	Sub	1170	C=1.0000	T=0.0000
1000Genomes_30x	American	Sub	980	C=0.992	T=0.008
1000Genomes	Global	Study-wide	5008	C=0.9902	T=0.0098
1000Genomes	African	Sub	1322	C=0.9977	T=0.0023
1000Genomes	East Asian	Sub	1008	C=1.0000	T=0.0000
1000Genomes	Europe	Sub	1006	C=0.9642	T=0.0358
1000Genomes	South Asian	Sub	978	C=0.997	T=0.003
1000Genomes	American	Sub	694	C=0.990	T=0.010
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9558	T=0.0442
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9676	T=0.0324
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9736	T=0.0264
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9997	T=0.0003
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9995	T=0.0005
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.971	T=0.029
Northern Sweden	ACPOP	Study-wide	600	C=0.950	T=0.050
The Danish reference pan genome	Danish	Study-wide	40	C=0.97	T=0.03
SGDP_PRJ	Global	Study-wide	16	C=0.44	T=0.56

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.53934586C>T
GRCh37.p13 chr 1	NC_000001.10:g.54400259C>T

Gene: HSPB11, heat shock protein family B (small) member 11 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
IFT25 transcript variant 2	NM_001316935.2:c.99-4441G… NM_001316935.2:c.99-4441G>A	N/A	Intron Variant
IFT25 transcript variant 5	NM_001382249.1:c.99-4441G… NM_001382249.1:c.99-4441G>A	N/A	Intron Variant
IFT25 transcript variant 6	NM_001382250.1:c.99-4441G… NM_001382250.1:c.99-4441G>A	N/A	Intron Variant
IFT25 transcript variant 7	NM_001382251.1:c.-31-4441… NM_001382251.1:c.-31-4441G>A	N/A	Intron Variant
IFT25 transcript variant 8	NM_001382252.1:c.-31-4441… NM_001382252.1:c.-31-4441G>A	N/A	Intron Variant
IFT25 transcript variant 9	NM_001382253.1:c.99-4441G… NM_001382253.1:c.99-4441G>A	N/A	Intron Variant
IFT25 transcript variant 10	NM_001382254.1:c.-31-4441… NM_001382254.1:c.-31-4441G>A	N/A	Intron Variant
IFT25 transcript variant 18	NM_001382261.1:c.99-4441G… NM_001382261.1:c.99-4441G>A	N/A	Intron Variant
IFT25 transcript variant 1	NM_016126.4:c.99-4441G>A	N/A	Intron Variant
IFT25 transcript variant 3	NR_133632.2:n.	N/A	Intron Variant
IFT25 transcript variant 4	NR_133633.2:n.	N/A	Intron Variant
IFT25 transcript variant 11	NR_167989.1:n.	N/A	Intron Variant
IFT25 transcript variant 12	NR_167990.1:n.	N/A	Intron Variant
IFT25 transcript variant 13	NR_167991.1:n.	N/A	Intron Variant
IFT25 transcript variant 14	NR_167992.1:n.	N/A	Intron Variant
IFT25 transcript variant 15	NR_167993.1:n.	N/A	Intron Variant
IFT25 transcript variant 16	NR_167994.1:n.	N/A	Intron Variant
IFT25 transcript variant 17	NR_167995.1:n.	N/A	Intron Variant
IFT25 transcript variant X1	XM_047422519.1:c.99-4441G… XM_047422519.1:c.99-4441G>A	N/A	Intron Variant
IFT25 transcript variant X2	XM_047422520.1:c.99-4441G… XM_047422520.1:c.99-4441G>A	N/A	Intron Variant
IFT25 transcript variant X3	XM_047422521.1:c.99-4441G… XM_047422521.1:c.99-4441G>A	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	C=	T
GRCh38.p14 chr 1	NC_000001.11:g.53934586=	NC_000001.11:g.53934586C>T
GRCh37.p13 chr 1	NC_000001.10:g.54400259=	NC_000001.10:g.54400259C>T
IFT25 transcript variant 2	NM_001316935.2:c.99-4441=	NM_001316935.2:c.99-4441G>A
IFT25 transcript variant 5	NM_001382249.1:c.99-4441=	NM_001382249.1:c.99-4441G>A
IFT25 transcript variant 6	NM_001382250.1:c.99-4441=	NM_001382250.1:c.99-4441G>A
IFT25 transcript variant 7	NM_001382251.1:c.-31-4441=	NM_001382251.1:c.-31-4441G>A
IFT25 transcript variant 8	NM_001382252.1:c.-31-4441=	NM_001382252.1:c.-31-4441G>A
IFT25 transcript variant 9	NM_001382253.1:c.99-4441=	NM_001382253.1:c.99-4441G>A
IFT25 transcript variant 10	NM_001382254.1:c.-31-4441=	NM_001382254.1:c.-31-4441G>A
IFT25 transcript variant 18	NM_001382261.1:c.99-4441=	NM_001382261.1:c.99-4441G>A
HSPB11 transcript	NM_016126.2:c.99-4441=	NM_016126.2:c.99-4441G>A
IFT25 transcript variant 1	NM_016126.4:c.99-4441=	NM_016126.4:c.99-4441G>A
HSPB11 transcript variant X1	XM_005270942.1:c.99-4441=	XM_005270942.1:c.99-4441G>A
HSPB11 transcript variant X2	XM_005270943.1:c.99-4441=	XM_005270943.1:c.99-4441G>A
IFT25 transcript variant X1	XM_047422519.1:c.99-4441=	XM_047422519.1:c.99-4441G>A
IFT25 transcript variant X2	XM_047422520.1:c.99-4441=	XM_047422520.1:c.99-4441G>A
IFT25 transcript variant X3	XM_047422521.1:c.99-4441=	XM_047422521.1:c.99-4441G>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#.

29 SubSNP, 14 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss230531215	Jul 14, 2010 (132)
2	GMI	ss284048488	Apr 25, 2013 (138)
3	EVA-GONL	ss975152043	Aug 21, 2014 (142)
4	1000GENOMES	ss1290862198	Aug 21, 2014 (142)
5	EVA_GENOME_DK	ss1574053145	Apr 01, 2015 (144)
6	EVA_DECODE	ss1584518103	Apr 01, 2015 (144)
7	EVA_UK10K_ALSPAC	ss1600157180	Apr 01, 2015 (144)
8	EVA_UK10K_TWINSUK	ss1643151213	Apr 01, 2015 (144)
9	JJLAB	ss2019695473	Sep 14, 2016 (149)
10	HUMAN_LONGEVITY	ss2162442751	Dec 20, 2016 (150)
11	GNOMAD	ss2755068235	Nov 08, 2017 (151)
12	SWEGEN	ss2986804612	Nov 08, 2017 (151)
13	CSHL	ss3343449888	Nov 08, 2017 (151)
14	EGCUT_WGS	ss3654868235	Jul 12, 2019 (153)
15	EVA_DECODE	ss3686756000	Jul 12, 2019 (153)
16	ACPOP	ss3727039825	Jul 12, 2019 (153)
17	EVA	ss3746193506	Jul 12, 2019 (153)
18	SGDP_PRJ	ss3848830087	Apr 25, 2020 (154)
19	KRGDB	ss3893838327	Apr 25, 2020 (154)
20	KOGIC	ss3944495170	Apr 25, 2020 (154)
21	TOPMED	ss4449489321	Apr 25, 2021 (155)
22	1000G_HIGH_COVERAGE	ss5242242750	Oct 12, 2022 (156)
23	EVA	ss5318675680	Oct 12, 2022 (156)
24	HUGCELL_USP	ss5443306909	Oct 12, 2022 (156)
25	1000G_HIGH_COVERAGE	ss5514506643	Oct 12, 2022 (156)
26	SANFORD_IMAGENETICS	ss5625513494	Oct 12, 2022 (156)
27	EVA	ss5831948326	Oct 12, 2022 (156)
28	EVA	ss5908228629	Oct 12, 2022 (156)
29	EVA	ss5937344563	Oct 12, 2022 (156)
30	1000Genomes	NC_000001.10 - 54400259	Oct 11, 2018 (152)
31	1000Genomes_30x	NC_000001.11 - 53934586	Oct 12, 2022 (156)
32	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 54400259	Oct 11, 2018 (152)
33	Genetic variation in the Estonian population	NC_000001.10 - 54400259	Oct 11, 2018 (152)
34	The Danish reference pan genome	NC_000001.10 - 54400259	Apr 25, 2020 (154)
35	gnomAD - Genomes	NC_000001.11 - 53934586	Apr 25, 2021 (155)
36	Genome of the Netherlands Release 5	NC_000001.10 - 54400259	Apr 25, 2020 (154)
37	KOREAN population from KRGDB	NC_000001.10 - 54400259	Apr 25, 2020 (154)
38	Korean Genome Project	NC_000001.11 - 53934586	Apr 25, 2020 (154)
39	Northern Sweden	NC_000001.10 - 54400259	Jul 12, 2019 (153)
40	SGDP_PRJ	NC_000001.10 - 54400259	Apr 25, 2020 (154)
41	TopMed	NC_000001.11 - 53934586	Apr 25, 2021 (155)
42	UK 10K study - Twins	NC_000001.10 - 54400259	Oct 11, 2018 (152)
43	ALFA	NC_000001.11 - 53934586	Apr 25, 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
ss284048488, ss1584518103	NC_000001.9:54172846:C:T	NC_000001.11:53934585:C:T	(self)
1579463, 858497, 606483, 1498221, 363768, 1015721, 324690, 847067, 858497, ss230531215, ss975152043, ss1290862198, ss1574053145, ss1600157180, ss1643151213, ss2019695473, ss2755068235, ss2986804612, ss3343449888, ss3654868235, ss3727039825, ss3746193506, ss3848830087, ss3893838327, ss5318675680, ss5625513494, ss5831948326, ss5937344563	NC_000001.10:54400258:C:T	NC_000001.11:53934585:C:T	(self)
2032578, 11188050, 873171, 13095656, 13184537007, ss2162442751, ss3686756000, ss3944495170, ss4449489321, ss5242242750, ss5443306909, ss5514506643, ss5908228629	NC_000001.11:53934585:C:T	NC_000001.11:53934585:C: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 rs116124913

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

rs116124913