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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.

rs55738309

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:17823118 (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=0.002685 (591/220132, ALFA)
A=0.001697 (238/140266, GnomAD)
A=0.002134 (259/121374, ExAC) (+ 9 more)
A=0.00038 (30/78698, PAGE_STUDY)
A=0.00269 (35/13006, GO-ESP)
A=0.0006 (3/5008, 1000G)
A=0.0018 (8/4480, Estonian)
A=0.0034 (13/3854, ALSPAC)
A=0.0043 (16/3708, TWINSUK)
A=0.008 (8/998, GoNL)
A=0.002 (1/600, NorthernSweden)
A=0.002 (1/534, MGP)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ACTL8 : Missense 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.17823118C>A
GRCh38.p13 chr 1 NC_000001.11:g.17823118C>T
GRCh37.p13 chr 1 NC_000001.10:g.18149613C>A
GRCh37.p13 chr 1 NC_000001.10:g.18149613C>T
Gene: ACTL8, actin like 8 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ACTL8 transcript NM_030812.3:c.110C>A P [CCG] > Q [CAG] Coding Sequence Variant
actin-like protein 8 NP_110439.2:p.Pro37Gln P (Pro) > Q (Gln) Missense Variant
ACTL8 transcript NM_030812.3:c.110C>T P [CCG] > L [CTG] Coding Sequence Variant
actin-like protein 8 NP_110439.2:p.Pro37Leu P (Pro) > L (Leu) Missense Variant
ACTL8 transcript variant X1 XM_011542212.2:c.110C>A P [CCG] > Q [CAG] Coding Sequence Variant
actin-like protein 8 isoform X1 XP_011540514.1:p.Pro37Gln P (Pro) > Q (Gln) Missense Variant
ACTL8 transcript variant X1 XM_011542212.2:c.110C>T P [CCG] > L [CTG] Coding Sequence Variant
actin-like protein 8 isoform X1 XP_011540514.1:p.Pro37Leu P (Pro) > L (Leu) Missense 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 220132 C=0.997315 A=0.002685, T=0.000000
European Sub 190494 C=0.997150 A=0.002850, T=0.000000
African Sub 4960 C=0.9990 A=0.0010, T=0.0000
African Others Sub 176 C=1.000 A=0.000, T=0.000
African American Sub 4784 C=0.9990 A=0.0010, T=0.0000
Asian Sub 6394 C=1.0000 A=0.0000, T=0.0000
East Asian Sub 4546 C=1.0000 A=0.0000, T=0.0000
Other Asian Sub 1848 C=1.0000 A=0.0000, T=0.0000
Latin American 1 Sub 796 C=1.000 A=0.000, T=0.000
Latin American 2 Sub 968 C=1.000 A=0.000, T=0.000
South Asian Sub 280 C=0.996 A=0.004, T=0.000
Other Sub 16240 C=0.99741 A=0.00259, T=0.00000


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
gnomAD - Genomes Global Study-wide 140266 C=0.998303 A=0.001697
gnomAD - Genomes European Sub 75958 C=0.99755 A=0.00245
gnomAD - Genomes African Sub 42044 C=0.99948 A=0.00052
gnomAD - Genomes American Sub 13658 C=0.99993 A=0.00007
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=0.9928 A=0.0072
gnomAD - Genomes East Asian Sub 3134 C=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2148 C=0.9977 A=0.0023
ExAC Global Study-wide 121374 C=0.997866 A=0.002134
ExAC Europe Sub 73330 C=0.99656 A=0.00344
ExAC Asian Sub 25160 C=1.00000 A=0.00000
ExAC American Sub 11576 C=0.99991 A=0.00009
ExAC African Sub 10402 C=0.99942 A=0.00058
ExAC Other Sub 906 C=1.000 A=0.000
The PAGE Study Global Study-wide 78698 C=0.99962 A=0.00038
The PAGE Study AfricanAmerican Sub 32514 C=0.99935 A=0.00065
The PAGE Study Mexican Sub 10810 C=0.99991 A=0.00009
The PAGE Study Asian Sub 8318 C=1.0000 A=0.0000
The PAGE Study PuertoRican Sub 7918 C=0.9999 A=0.0001
The PAGE Study NativeHawaiian Sub 4534 C=0.9998 A=0.0002
The PAGE Study Cuban Sub 4228 C=1.0000 A=0.0000
The PAGE Study Dominican Sub 3828 C=0.9997 A=0.0003
The PAGE Study CentralAmerican Sub 2450 C=1.0000 A=0.0000
The PAGE Study SouthAmerican Sub 1982 C=0.9995 A=0.0005
The PAGE Study NativeAmerican Sub 1260 C=0.9968 A=0.0032
The PAGE Study SouthAsian Sub 856 C=1.000 A=0.000
GO Exome Sequencing Project Global Study-wide 13006 C=0.99731 A=0.00269
GO Exome Sequencing Project European American Sub 8600 C=0.9964 A=0.0036
GO Exome Sequencing Project African American Sub 4406 C=0.9991 A=0.0009
1000Genomes Global Study-wide 5008 C=0.9994 A=0.0006
1000Genomes African Sub 1322 C=1.0000 A=0.0000
1000Genomes East Asian Sub 1008 C=1.0000 A=0.0000
1000Genomes Europe Sub 1006 C=0.9970 A=0.0030
1000Genomes South Asian Sub 978 C=1.000 A=0.000
1000Genomes American Sub 694 C=1.000 A=0.000
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9982 A=0.0018
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9966 A=0.0034
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9957 A=0.0043
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.992 A=0.008
Northern Sweden ACPOP Study-wide 600 C=0.998 A=0.002
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.998 A=0.002
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 1 NC_000001.11:g.17823118= NC_000001.11:g.17823118C>A NC_000001.11:g.17823118C>T
GRCh37.p13 chr 1 NC_000001.10:g.18149613= NC_000001.10:g.18149613C>A NC_000001.10:g.18149613C>T
ACTL8 transcript NM_030812.3:c.110= NM_030812.3:c.110C>A NM_030812.3:c.110C>T
ACTL8 transcript NM_030812.2:c.110= NM_030812.2:c.110C>A NM_030812.2:c.110C>T
ACTL8 transcript variant X1 XM_011542212.2:c.110= XM_011542212.2:c.110C>A XM_011542212.2:c.110C>T
actin-like protein 8 NP_110439.2:p.Pro37= NP_110439.2:p.Pro37Gln NP_110439.2:p.Pro37Leu
actin-like protein 8 isoform X1 XP_011540514.1:p.Pro37= XP_011540514.1:p.Pro37Gln XP_011540514.1:p.Pro37Leu
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#.

51 SubSNP, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 SI_EXO ss76884806 Dec 06, 2007 (129)
2 1000GENOMES ss217314457 Jul 14, 2010 (132)
3 NHLBI-ESP ss341939369 May 09, 2011 (134)
4 1000GENOMES ss453906642 Sep 17, 2011 (135)
5 1000GENOMES ss489724887 May 04, 2012 (137)
6 EXOME_CHIP ss491287945 May 04, 2012 (137)
7 CLINSEQ_SNP ss491587203 May 04, 2012 (137)
8 ILLUMINA ss780806813 Sep 08, 2015 (146)
9 ILLUMINA ss783488496 Sep 08, 2015 (146)
10 EVA-GONL ss974903810 Aug 21, 2014 (142)
11 1000GENOMES ss1289872601 Aug 21, 2014 (142)
12 EVA_DECODE ss1584261092 Apr 01, 2015 (144)
13 EVA_UK10K_ALSPAC ss1599639507 Apr 01, 2015 (144)
14 EVA_UK10K_TWINSUK ss1642633540 Apr 01, 2015 (144)
15 EVA_EXAC ss1685351819 Apr 01, 2015 (144)
16 EVA_MGP ss1710892626 Apr 01, 2015 (144)
17 ILLUMINA ss1751884960 Sep 08, 2015 (146)
18 ILLUMINA ss1917723766 Feb 12, 2016 (147)
19 ILLUMINA ss1945986452 Feb 12, 2016 (147)
20 ILLUMINA ss1958247858 Feb 12, 2016 (147)
21 JJLAB ss2019568325 Sep 14, 2016 (149)
22 HUMAN_LONGEVITY ss2160392592 Dec 20, 2016 (150)
23 TOPMED ss2322573275 Dec 20, 2016 (150)
24 TOPMED ss2322573276 Dec 20, 2016 (150)
25 ILLUMINA ss2710666825 Nov 08, 2017 (151)
26 GNOMAD ss2731193580 Nov 08, 2017 (151)
27 GNOMAD ss2746240325 Nov 08, 2017 (151)
28 GNOMAD ss2752209887 Nov 08, 2017 (151)
29 AFFY ss2984847570 Nov 08, 2017 (151)
30 SWEGEN ss2986399139 Nov 08, 2017 (151)
31 ILLUMINA ss3021061144 Nov 08, 2017 (151)
32 TOPMED ss3069887014 Nov 08, 2017 (151)
33 TOPMED ss3069887015 Nov 08, 2017 (151)
34 ILLUMINA ss3626037665 Oct 11, 2018 (152)
35 ILLUMINA ss3634309796 Oct 11, 2018 (152)
36 ILLUMINA ss3640017160 Oct 11, 2018 (152)
37 ILLUMINA ss3644482303 Oct 11, 2018 (152)
38 ILLUMINA ss3651385666 Oct 11, 2018 (152)
39 ILLUMINA ss3653621310 Oct 11, 2018 (152)
40 EGCUT_WGS ss3654467825 Jul 12, 2019 (153)
41 EVA_DECODE ss3686261487 Jul 12, 2019 (153)
42 ILLUMINA ss3725001336 Jul 12, 2019 (153)
43 ACPOP ss3726832997 Jul 12, 2019 (153)
44 ILLUMINA ss3744340448 Jul 12, 2019 (153)
45 ILLUMINA ss3744610759 Jul 12, 2019 (153)
46 PAGE_CC ss3770789431 Jul 12, 2019 (153)
47 ILLUMINA ss3772112340 Jul 12, 2019 (153)
48 EVA ss3823569286 Apr 25, 2020 (154)
49 EVA ss3825555524 Apr 25, 2020 (154)
50 TOPMED ss4440758606 Apr 27, 2021 (155)
51 TOPMED ss4440758607 Apr 27, 2021 (155)
52 1000Genomes NC_000001.10 - 18149613 Oct 11, 2018 (152)
53 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 18149613 Oct 11, 2018 (152)
54 Genetic variation in the Estonian population NC_000001.10 - 18149613 Oct 11, 2018 (152)
55 ExAC NC_000001.10 - 18149613 Oct 11, 2018 (152)
56 gnomAD - Genomes NC_000001.11 - 17823118 Apr 27, 2021 (155)
57 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 206151 (NC_000001.10:18149612:C:C 250996/251472, NC_000001.10:18149612:C:A 476/251472)
Row 206152 (NC_000001.10:18149612:C:C 251471/251472, NC_000001.10:18149612:C:T 1/251472)

- Jul 12, 2019 (153)
58 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 206151 (NC_000001.10:18149612:C:C 250996/251472, NC_000001.10:18149612:C:A 476/251472)
Row 206152 (NC_000001.10:18149612:C:C 251471/251472, NC_000001.10:18149612:C:T 1/251472)

- Jul 12, 2019 (153)
59 GO Exome Sequencing Project NC_000001.10 - 18149613 Oct 11, 2018 (152)
60 Genome of the Netherlands Release 5 NC_000001.10 - 18149613 Apr 25, 2020 (154)
61 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 18149613 Apr 25, 2020 (154)
62 Northern Sweden NC_000001.10 - 18149613 Jul 12, 2019 (153)
63 The PAGE Study NC_000001.11 - 17823118 Jul 12, 2019 (153)
64 TopMed

Submission ignored due to conflicting rows:
Row 4364941 (NC_000001.11:17823117:C:A 445/264690)
Row 4364942 (NC_000001.11:17823117:C:T 5/264690)

- Apr 27, 2021 (155)
65 TopMed

Submission ignored due to conflicting rows:
Row 4364941 (NC_000001.11:17823117:C:A 445/264690)
Row 4364942 (NC_000001.11:17823117:C:T 5/264690)

- Apr 27, 2021 (155)
66 UK 10K study - Twins NC_000001.10 - 18149613 Oct 11, 2018 (152)
67 ALFA NC_000001.11 - 17823118 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
ss217314457, ss491587203, ss1584261092 NC_000001.9:18022199:C:A NC_000001.11:17823117:C:A (self)
555241, 287515, 206073, 4534434, 28004, 125559, 9378, 117862, 287515, ss341939369, ss453906642, ss489724887, ss491287945, ss780806813, ss783488496, ss974903810, ss1289872601, ss1599639507, ss1642633540, ss1685351819, ss1710892626, ss1751884960, ss1917723766, ss1945986452, ss1958247858, ss2019568325, ss2322573275, ss2710666825, ss2731193580, ss2746240325, ss2752209887, ss2984847570, ss2986399139, ss3021061144, ss3626037665, ss3634309796, ss3640017160, ss3644482303, ss3651385666, ss3653621310, ss3654467825, ss3726832997, ss3744340448, ss3744610759, ss3772112340, ss3823569286, ss3825555524 NC_000001.10:18149612:C:A NC_000001.11:17823117:C:A (self)
3884681, 10900, 2740552, 14685907850, ss2160392592, ss3069887014, ss3686261487, ss3725001336, ss3770789431, ss4440758606 NC_000001.11:17823117:C:A NC_000001.11:17823117:C:A (self)
ss76884806 NT_004610.18:973954:C:A NC_000001.11:17823117:C:A (self)
ss2322573276, ss2731193580 NC_000001.10:18149612:C:T NC_000001.11:17823117:C:T (self)
2740552, 14685907850, ss3069887015, ss4440758607 NC_000001.11:17823117:C:T NC_000001.11:17823117: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 rs55738309

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