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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.

rs79643527

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr10:55268 (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
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000004 (1/264690, TOPMED)
T=0.000920 (129/140246, GnomAD)
T=0.00084 (14/16700, ALFA) (+ 4 more)
T=0.0004 (2/5008, 1000G)
T=0.003 (2/600, NorthernSweden)
C=0.5 (2/4, SGDP_PRJ)
T=0.5 (2/4, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TUBB8 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
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 10 NC_000010.11:g.55268C>A
GRCh38.p13 chr 10 NC_000010.11:g.55268C>T
GRCh37.p13 chr 10 NC_000010.10:g.101208C>A
GRCh37.p13 chr 10 NC_000010.10:g.101208C>T
TUBB8 RefSeqGene NG_046777.1:g.26188G>T
TUBB8 RefSeqGene NG_046777.1:g.26188G>A
GRCh37.p13 chr 10 fix patch HG905_PATCH NW_003571043.1:g.45268C>A
GRCh37.p13 chr 10 fix patch HG905_PATCH NW_003571043.1:g.45268C>T
Gene: TUBB8, tubulin beta 8 class VIII (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TUBB8 transcript variant 2 NM_001389618.1:c.-661-535…

NM_001389618.1:c.-661-5359G>T

N/A Intron Variant
TUBB8 transcript variant 3 NM_001389619.1:c.-985-503…

NM_001389619.1:c.-985-5035G>T

N/A Intron Variant
TUBB8 transcript variant 1 NM_177987.3:c. N/A Genic Upstream Transcript Variant
TUBB8 transcript variant X3 XM_011519460.2:c. N/A Genic Upstream Transcript Variant
TUBB8 transcript variant X1 XM_017016192.2:c. N/A Genic Upstream Transcript Variant
TUBB8 transcript variant X2 XM_017016193.2:c. N/A Genic Upstream Transcript 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

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 16700 C=0.99916 A=0.00000, T=0.00084
European Sub 12212 C=0.99885 A=0.00000, T=0.00115
African Sub 2864 C=1.0000 A=0.0000, T=0.0000
African Others Sub 108 C=1.000 A=0.000, T=0.000
African American Sub 2756 C=1.0000 A=0.0000, T=0.0000
Asian Sub 108 C=1.000 A=0.000, T=0.000
East Asian Sub 84 C=1.00 A=0.00, T=0.00
Other Asian Sub 24 C=1.00 A=0.00, T=0.00
Latin American 1 Sub 146 C=1.000 A=0.000, T=0.000
Latin American 2 Sub 610 C=1.000 A=0.000, T=0.000
South Asian Sub 94 C=1.00 A=0.00, T=0.00
Other Sub 666 C=1.000 A=0.000, T=0.000


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 C=0.999996 A=0.000004
gnomAD - Genomes Global Study-wide 140246 C=0.999080 T=0.000920
gnomAD - Genomes European Sub 75938 C=0.99837 T=0.00163
gnomAD - Genomes African Sub 42052 C=1.00000 T=0.00000
gnomAD - Genomes American Sub 13654 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=0.9994 T=0.0006
gnomAD - Genomes East Asian Sub 3126 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2152 C=0.9986 T=0.0014
Allele Frequency Aggregator Total Global 16700 C=0.99916 A=0.00000, T=0.00084
Allele Frequency Aggregator European Sub 12212 C=0.99885 A=0.00000, T=0.00115
Allele Frequency Aggregator African Sub 2864 C=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator Other Sub 666 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 108 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 94 C=1.00 A=0.00, T=0.00
1000Genomes Global Study-wide 5008 C=0.9996 T=0.0004
1000Genomes African Sub 1322 C=1.0000 T=0.0000
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=0.9980 T=0.0020
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=1.000 T=0.000
Northern Sweden ACPOP Study-wide 600 C=0.997 T=0.003
SGDP_PRJ Global Study-wide 4 C=0.5 T=0.5
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 C= A T
GRCh38.p13 chr 10 NC_000010.11:g.55268= NC_000010.11:g.55268C>A NC_000010.11:g.55268C>T
GRCh37.p13 chr 10 NC_000010.10:g.101208= NC_000010.10:g.101208C>A NC_000010.10:g.101208C>T
TUBB8 RefSeqGene NG_046777.1:g.26188= NG_046777.1:g.26188G>T NG_046777.1:g.26188G>A
GRCh37.p13 chr 10 fix patch HG905_PATCH NW_003571043.1:g.45268= NW_003571043.1:g.45268C>A NW_003571043.1:g.45268C>T
TUBB8 transcript variant 2 NM_001389618.1:c.-661-5359= NM_001389618.1:c.-661-5359G>T NM_001389618.1:c.-661-5359G>A
TUBB8 transcript variant 3 NM_001389619.1:c.-985-5035= NM_001389619.1:c.-985-5035G>T NM_001389619.1:c.-985-5035G>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#.

10 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 ILLUMINA-UK ss118963173 Dec 01, 2009 (131)
2 1000GENOMES ss1335911964 Aug 21, 2014 (142)
3 GNOMAD ss2884515320 Oct 12, 2018 (152)
4 SWEGEN ss3005783430 Oct 12, 2018 (152)
5 TOPMED ss3109324926 Nov 08, 2017 (151)
6 EVA_DECODE ss3689094899 Jul 13, 2019 (153)
7 ACPOP ss3736974108 Jul 13, 2019 (153)
8 SGDP_PRJ ss3873325935 Apr 26, 2020 (154)
9 GNOMAD ss4211403387 Apr 26, 2021 (155)
10 TOPMED ss4839516332 Apr 26, 2021 (155)
11 1000Genomes NC_000010.10 - 101208 Oct 12, 2018 (152)
12 gnomAD - Genomes NC_000010.11 - 55268 Apr 26, 2021 (155)
13 Northern Sweden NC_000010.10 - 101208 Jul 13, 2019 (153)
14 SGDP_PRJ NC_000010.10 - 101208 Apr 26, 2020 (154)
15 TopMed NC_000010.11 - 55268 Apr 26, 2021 (155)
16 ALFA NC_000010.11 - 55268 Apr 26, 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
55061987, 268565692, ss4839516332 NC_000010.11:55267:C:A NC_000010.11:55267:C:A
ss118963173 NC_000010.9:91207:C:T NC_000010.11:55267:C:T (self)
48245634, 10258973, 25342915, ss1335911964, ss2884515320, ss3005783430, ss3736974108, ss3873325935 NC_000010.10:101207:C:T NC_000010.11:55267:C:T (self)
340926559, 268565692, ss3109324926, ss3689094899, ss4211403387 NC_000010.11:55267:C:T NC_000010.11:55267:C: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 rs79643527

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.post596+ae089ad