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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.

rs116745746

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:17825901 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000193 (51/264690, TOPMED)
T=0.000792 (198/250086, GnomAD_exome)
T=0.000214 (30/140308, GnomAD) (+ 5 more)
T=0.000796 (96/120644, ExAC)
T=0.00027 (12/44662, ALFA)
T=0.00023 (3/13006, GO-ESP)
T=0.0012 (6/5008, 1000G)
T=0.0005 (1/1828, Korea1K)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ACTL8 : Synonymous 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 1 NC_000001.11:g.17825901C>T
GRCh37.p13 chr 1 NC_000001.10:g.18152396C>T
Gene: ACTL8, actin like 8 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ACTL8 transcript NM_030812.3:c.483C>T H [CAC] > H [CAT] Coding Sequence Variant
actin-like protein 8 NP_110439.2:p.His161= H (His) > H (His) Synonymous Variant
ACTL8 transcript variant X1 XM_011542212.2:c.483C>T H [CAC] > H [CAT] Coding Sequence Variant
actin-like protein 8 isoform X1 XP_011540514.1:p.His161= H (His) > H (His) Synonymous 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 44662 C=0.99973 T=0.00027
European Sub 32686 C=0.99972 T=0.00028
African Sub 3560 C=1.0000 T=0.0000
African Others Sub 122 C=1.000 T=0.000
African American Sub 3438 C=1.0000 T=0.0000
Asian Sub 168 C=1.000 T=0.000
East Asian Sub 112 C=1.000 T=0.000
Other Asian Sub 56 C=1.00 T=0.00
Latin American 1 Sub 494 C=1.000 T=0.000
Latin American 2 Sub 628 C=1.000 T=0.000
South Asian Sub 98 C=1.00 T=0.00
Other Sub 7028 C=0.9996 T=0.0004


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").

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Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 C=0.999807 T=0.000193
gnomAD - Exomes Global Study-wide 250086 C=0.999208 T=0.000792
gnomAD - Exomes European Sub 134176 C=0.999747 T=0.000253
gnomAD - Exomes Asian Sub 48984 C=0.99720 T=0.00280
gnomAD - Exomes American Sub 34556 C=0.99954 T=0.00046
gnomAD - Exomes African Sub 16196 C=0.99988 T=0.00012
gnomAD - Exomes Ashkenazi Jewish Sub 10058 C=0.99960 T=0.00040
gnomAD - Exomes Other Sub 6116 C=0.9992 T=0.0008
gnomAD - Genomes Global Study-wide 140308 C=0.999786 T=0.000214
gnomAD - Genomes European Sub 75962 C=0.99983 T=0.00017
gnomAD - Genomes African Sub 42074 C=0.99993 T=0.00007
gnomAD - Genomes American Sub 13666 C=0.99898 T=0.00102
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3132 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2150 C=1.0000 T=0.0000
ExAC Global Study-wide 120644 C=0.999204 T=0.000796
ExAC Europe Sub 72834 C=0.99975 T=0.00025
ExAC Asian Sub 25126 C=0.99705 T=0.00295
ExAC American Sub 11498 C=1.00000 T=0.00000
ExAC African Sub 10290 C=0.99981 T=0.00019
ExAC Other Sub 896 C=0.998 T=0.002
GO Exome Sequencing Project Global Study-wide 13006 C=0.99977 T=0.00023
GO Exome Sequencing Project European American Sub 8600 C=0.9998 T=0.0002
GO Exome Sequencing Project African American Sub 4406 C=0.9998 T=0.0002
1000Genomes Global Study-wide 5008 C=0.9988 T=0.0012
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=0.996 T=0.004
1000Genomes American Sub 694 C=1.000 T=0.000
Korean Genome Project KOREAN Study-wide 1828 C=0.9995 T=0.0005
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= T
GRCh38.p13 chr 1 NC_000001.11:g.17825901= NC_000001.11:g.17825901C>T
GRCh37.p13 chr 1 NC_000001.10:g.18152396= NC_000001.10:g.18152396C>T
ACTL8 transcript NM_030812.3:c.483= NM_030812.3:c.483C>T
ACTL8 transcript NM_030812.2:c.483= NM_030812.2:c.483C>T
ACTL8 transcript variant X1 XM_011542212.2:c.483= XM_011542212.2:c.483C>T
actin-like protein 8 NP_110439.2:p.His161= NP_110439.2:p.His161=
actin-like protein 8 isoform X1 XP_011540514.1:p.His161= XP_011540514.1:p.His161=
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#.

15 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss217410578 Jul 14, 2010 (132)
2 1000GENOMES ss328449532 May 09, 2011 (134)
3 NHLBI-ESP ss341939384 May 09, 2011 (134)
4 CLINSEQ_SNP ss491587208 May 04, 2012 (137)
5 1000GENOMES ss1289872675 Aug 21, 2014 (142)
6 EVA_EXAC ss1685351906 Apr 01, 2015 (144)
7 HUMAN_LONGEVITY ss2160392755 Dec 20, 2016 (150)
8 TOPMED ss2322573466 Dec 20, 2016 (150)
9 GNOMAD ss2731193708 Nov 08, 2017 (151)
10 GNOMAD ss2746240361 Nov 08, 2017 (151)
11 GNOMAD ss2752210126 Nov 08, 2017 (151)
12 TOPMED ss3069887516 Nov 08, 2017 (151)
13 EVA ss3823569308 Apr 25, 2020 (154)
14 KOGIC ss3943943341 Apr 25, 2020 (154)
15 TOPMED ss4440759333 Apr 27, 2021 (155)
16 1000Genomes NC_000001.10 - 18152396 Oct 11, 2018 (152)
17 ExAC NC_000001.10 - 18152396 Oct 11, 2018 (152)
18 gnomAD - Genomes NC_000001.11 - 17825901 Apr 27, 2021 (155)
19 gnomAD - Exomes NC_000001.10 - 18152396 Jul 12, 2019 (153)
20 GO Exome Sequencing Project NC_000001.10 - 18152396 Oct 11, 2018 (152)
21 Korean Genome Project NC_000001.11 - 17825901 Apr 25, 2020 (154)
22 TopMed NC_000001.11 - 17825901 Apr 27, 2021 (155)
23 ALFA NC_000001.11 - 17825901 Apr 27, 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
ss217410578, ss491587208 NC_000001.9:18024982:C:T NC_000001.11:17825900:C:T (self)
555321, 4534524, 206297, 28026, ss328449532, ss341939384, ss1289872675, ss1685351906, ss2322573466, ss2731193708, ss2746240361, ss2752210126, ss3823569308 NC_000001.10:18152395:C:T NC_000001.11:17825900:C:T (self)
3885243, 321342, 2740998, 4365668, 8091334304, ss2160392755, ss3069887516, ss3943943341, ss4440759333 NC_000001.11:17825900:C:T NC_000001.11:17825900: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 rs116745746

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