Name: rs9952365
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.

rs9952365

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr18:74525 (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: T>A / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.334304 (44639/133528, GnomAD)
T=0.02580 (729/28254, 14KJPN)
T=0.02524 (423/16756, 8.3KJPN) (+ 8 more)
T=0.4679 (2597/5550, ALFA)
T=0.1414 (414/2928, KOREAN)
T=0.0715 (131/1832, Korea1K)
T=0.304 (182/598, NorthernSweden)
T=0.158 (83/524, SGDP_PRJ)
T=0.333 (72/216, Qatari)
T=0.23 (9/40, GENOME_DK)
T=0.17 (4/24, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TUBB8B : 2KB Upstream 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	5550	T=0.4679	A=0.5321, G=0.0000
European	Sub	5308	T=0.4450	A=0.5550, G=0.0000
African	Sub	104	T=1.000	A=0.000, G=0.000
African Others	Sub	2	T=1.0	A=0.0, G=0.0
African American	Sub	102	T=1.000	A=0.000, G=0.000
Asian	Sub	0	T=0	A=0, G=0
East Asian	Sub	0	T=0	A=0, G=0
Other Asian	Sub	0	T=0	A=0, G=0
Latin American 1	Sub	18	T=1.00	A=0.00, G=0.00
Latin American 2	Sub	56	T=1.00	A=0.00, G=0.00
South Asian	Sub	4	T=1.0	A=0.0, G=0.0
Other	Sub	60	T=0.88	A=0.12, G=0.00

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
gnomAD - Genomes	Global	Study-wide	133528	T=0.334304	A=0.665696
gnomAD - Genomes	European	Sub	73112	T=0.36015	A=0.63985
gnomAD - Genomes	African	Sub	38948	T=0.29034	A=0.70966
gnomAD - Genomes	American	Sub	13110	T=0.37521	A=0.62479
gnomAD - Genomes	Ashkenazi Jewish	Sub	3234	T=0.4032	A=0.5968
gnomAD - Genomes	East Asian	Sub	3070	T=0.0322	A=0.9678
gnomAD - Genomes	Other	Sub	2054	T=0.3301	A=0.6699
14KJPN	JAPANESE	Study-wide	28254	T=0.02580	A=0.97420
8.3KJPN	JAPANESE	Study-wide	16756	T=0.02524	A=0.97476
Allele Frequency Aggregator	Total	Global	5550	T=0.4679	A=0.5321, G=0.0000
Allele Frequency Aggregator	European	Sub	5308	T=0.4450	A=0.5550, G=0.0000
Allele Frequency Aggregator	African	Sub	104	T=1.000	A=0.000, G=0.000
Allele Frequency Aggregator	Other	Sub	60	T=0.88	A=0.12, G=0.00
Allele Frequency Aggregator	Latin American 2	Sub	56	T=1.00	A=0.00, G=0.00
Allele Frequency Aggregator	Latin American 1	Sub	18	T=1.00	A=0.00, G=0.00
Allele Frequency Aggregator	South Asian	Sub	4	T=1.0	A=0.0, G=0.0
Allele Frequency Aggregator	Asian	Sub	0	T=0	A=0, G=0
KOREAN population from KRGDB	KOREAN	Study-wide	2928	T=0.1414	A=0.8586
Korean Genome Project	KOREAN	Study-wide	1832	T=0.0715	A=0.9285
Northern Sweden	ACPOP	Study-wide	598	T=0.304	A=0.696
SGDP_PRJ	Global	Study-wide	524	T=0.158	A=0.842
Qatari	Global	Study-wide	216	T=0.333	A=0.667
The Danish reference pan genome	Danish	Study-wide	40	T=0.23	A=0.78
Siberian	Global	Study-wide	24	T=0.17	A=0.83

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 18	NC_000018.10:g.74525T>A
GRCh38.p14 chr 18	NC_000018.10:g.74525T>G
GRCh37.p13 chr 18	NC_000018.9:g.74525T>A
GRCh37.p13 chr 18	NC_000018.9:g.74525T>G

Gene: TUBB8B, tubulin beta 8B (minus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
TUBB8B transcript variant 2	NM_001389609.1:c.	N/A	Upstream Transcript Variant
TUBB8B transcript variant 3	NM_001389610.1:c.	N/A	Upstream Transcript Variant
TUBB8B transcript variant 1	NM_001358689.2:c.	N/A	N/A
TUBB8B transcript variant X1	XM_024451143.2:c.	N/A	Upstream Transcript Variant
TUBB8B transcript variant X2	XM_024451144.2:c.	N/A	N/A
TUBB8B transcript variant X3	XM_024451146.2:c.	N/A	N/A
TUBB8B transcript variant X4	XM_024451147.2:c.	N/A	N/A
TUBB8B transcript variant X5	XM_024451148.2:c.	N/A	N/A

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	T=	A	G
GRCh38.p14 chr 18	NC_000018.10:g.74525=	NC_000018.10:g.74525T>A	NC_000018.10:g.74525T>G
GRCh37.p13 chr 18	NC_000018.9:g.74525=	NC_000018.9:g.74525T>A	NC_000018.9:g.74525T>G

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#.

39 SubSNP, 11 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss13792500	Dec 05, 2003 (119)
2	SSAHASNP	ss35483928	May 24, 2005 (125)
3	HGSV	ss77329905	Dec 06, 2007 (131)
4	BCMHGSC_JDW	ss90683138	Mar 24, 2008 (131)
5	HUMANGENOME_JCVI	ss96318596	Feb 05, 2009 (131)
6	ILLUMINA-UK	ss117754884	Dec 01, 2009 (131)
7	ENSEMBL	ss137217596	Dec 01, 2009 (131)
8	GMI	ss287226614	Apr 25, 2013 (138)
9	1000GENOMES	ss339893917	May 09, 2011 (134)
10	EVA-GONL	ss993404781	Aug 21, 2014 (142)
11	DDI	ss1428118253	Apr 01, 2015 (144)
12	EVA_GENOME_DK	ss1578273139	Apr 01, 2015 (144)
13	WEILL_CORNELL_DGM	ss1936874706	Feb 12, 2016 (147)
14	USC_VALOUEV	ss2157701062	Dec 20, 2016 (150)
15	GRF	ss2702268904	Nov 08, 2017 (151)
16	SWEGEN	ss3016021255	Nov 08, 2017 (151)
17	CSHL	ss3351876179	Nov 08, 2017 (151)
18	BIOINF_KMB_FNS_UNIBA	ss3645469797	Oct 12, 2018 (152)
19	URBANLAB	ss3650720202	Oct 12, 2018 (152)
20	EVA_DECODE	ss3701059699	Jul 13, 2019 (153)
21	ACPOP	ss3742278741	Jul 13, 2019 (153)
22	EVA	ss3755020531	Jul 13, 2019 (153)
23	PACBIO	ss3788286974	Jul 13, 2019 (153)
24	PACBIO	ss3793230186	Jul 13, 2019 (153)
25	PACBIO	ss3798116375	Jul 13, 2019 (153)
26	KHV_HUMAN_GENOMES	ss3820282488	Jul 13, 2019 (153)
27	EVA	ss3835014441	Apr 27, 2020 (154)
28	EVA	ss3846619409	Apr 27, 2020 (154)
29	SGDP_PRJ	ss3886374601	Apr 27, 2020 (154)
30	KRGDB	ss3936174672	Apr 27, 2020 (154)
31	KOGIC	ss3979448169	Apr 27, 2020 (154)
32	GNOMAD	ss4316833252	Apr 26, 2021 (155)
33	TOMMO_GENOMICS	ss5223808720	Apr 26, 2021 (155)
34	1000G_HIGH_COVERAGE	ss5304188658	Oct 16, 2022 (156)
35	HUGCELL_USP	ss5497122471	Oct 16, 2022 (156)
36	TOMMO_GENOMICS	ss5780473017	Oct 16, 2022 (156)
37	EVA	ss5827127576	Oct 16, 2022 (156)
38	EVA	ss5952081009	Oct 16, 2022 (156)
39	EVA	ss5980990464	Oct 16, 2022 (156)
40	The Danish reference pan genome	NC_000018.9 - 74525	Apr 27, 2020 (154)
41	gnomAD - Genomes	NC_000018.10 - 74525	Apr 26, 2021 (155)
42	KOREAN population from KRGDB	NC_000018.9 - 74525	Apr 27, 2020 (154)
43	Korean Genome Project	NC_000018.10 - 74525	Apr 27, 2020 (154)
44	Northern Sweden	NC_000018.9 - 74525	Jul 13, 2019 (153)
45	Qatari	NC_000018.9 - 74525	Apr 27, 2020 (154)
46	SGDP_PRJ	NC_000018.9 - 74525	Apr 27, 2020 (154)
47	Siberian	NC_000018.9 - 74525	Apr 27, 2020 (154)
48	8.3KJPN	NC_000018.9 - 74525	Apr 26, 2021 (155)
49	14KJPN	NC_000018.10 - 74525	Oct 16, 2022 (156)
50	ALFA	NC_000018.10 - 74525	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).

Associated ID	History Updated (Build)
rs55915854	Dec 02, 2009 (131)
rs62076666	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss35483928, ss77329905, ss90683138, ss117754884, ss287226614	NC_000018.8:64524:T:A	NC_000018.10:74524:T:A	(self)
4470570, 43352066, 15563606, 18916628, 38391581, 10217416, 81778027, ss339893917, ss993404781, ss1428118253, ss1578273139, ss1936874706, ss2157701062, ss2702268904, ss3016021255, ss3351876179, ss3742278741, ss3755020531, ss3788286974, ss3793230186, ss3798116375, ss3835014441, ss3886374601, ss3936174672, ss5223808720, ss5827127576, ss5952081009, ss5980990464	NC_000018.9:74524:T:A	NC_000018.10:74524:T:A	(self)
515810907, 35826170, 114310121, 12674314443, ss3645469797, ss3650720202, ss3701059699, ss3820282488, ss3846619409, ss3979448169, ss4316833252, ss5304188658, ss5497122471, ss5780473017	NC_000018.10:74524:T:A	NC_000018.10:74524:T:A	(self)
ss13792500	NT_010859.13:64524:T:A	NC_000018.10:74524:T:A	(self)
ss96318596, ss137217596	NT_010859.14:64524:T:A	NC_000018.10:74524:T:A	(self)
12674314443	NC_000018.10:74524:T:G	NC_000018.10:74524:T:G	(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 rs9952365

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

rs9952365