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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.

rs540514958

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr16:56357272-56357282 (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
del(A)4 / delA / dupA / dupAA / du…

del(A)4 / delA / dupA / dupAA / dupAAA

Variation Type
Indel Insertion and Deletion
Frequency
del(A)4=0.00000 (0/13900, ALFA)
delA=0.00000 (0/13900, ALFA)
dupA=0.00000 (0/13900, ALFA) (+ 3 more)
dupAA=0.00000 (0/13900, ALFA)
dupAAA=0.00000 (0/13900, ALFA)
delA=0.009 (9/998, GoNL)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GNAO1 : 3 Prime UTR 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 13900 AAAAAAAAAAA=1.00000 AAAAAAA=0.00000, AAAAAAAAAA=0.00000, AAAAAAAAAAAA=0.00000, AAAAAAAAAAAAA=0.00000, AAAAAAAAAAAAAA=0.00000
European Sub 9648 AAAAAAAAAAA=1.0000 AAAAAAA=0.0000, AAAAAAAAAA=0.0000, AAAAAAAAAAAA=0.0000, AAAAAAAAAAAAA=0.0000, AAAAAAAAAAAAAA=0.0000
African Sub 2834 AAAAAAAAAAA=1.0000 AAAAAAA=0.0000, AAAAAAAAAA=0.0000, AAAAAAAAAAAA=0.0000, AAAAAAAAAAAAA=0.0000, AAAAAAAAAAAAAA=0.0000
African Others Sub 110 AAAAAAAAAAA=1.000 AAAAAAA=0.000, AAAAAAAAAA=0.000, AAAAAAAAAAAA=0.000, AAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAA=0.000
African American Sub 2724 AAAAAAAAAAA=1.0000 AAAAAAA=0.0000, AAAAAAAAAA=0.0000, AAAAAAAAAAAA=0.0000, AAAAAAAAAAAAA=0.0000, AAAAAAAAAAAAAA=0.0000
Asian Sub 110 AAAAAAAAAAA=1.000 AAAAAAA=0.000, AAAAAAAAAA=0.000, AAAAAAAAAAAA=0.000, AAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAA=0.000
East Asian Sub 84 AAAAAAAAAAA=1.00 AAAAAAA=0.00, AAAAAAAAAA=0.00, AAAAAAAAAAAA=0.00, AAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAA=0.00
Other Asian Sub 26 AAAAAAAAAAA=1.00 AAAAAAA=0.00, AAAAAAAAAA=0.00, AAAAAAAAAAAA=0.00, AAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAA=0.00
Latin American 1 Sub 144 AAAAAAAAAAA=1.000 AAAAAAA=0.000, AAAAAAAAAA=0.000, AAAAAAAAAAAA=0.000, AAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAA=0.000
Latin American 2 Sub 604 AAAAAAAAAAA=1.000 AAAAAAA=0.000, AAAAAAAAAA=0.000, AAAAAAAAAAAA=0.000, AAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAA=0.000
South Asian Sub 84 AAAAAAAAAAA=1.00 AAAAAAA=0.00, AAAAAAAAAA=0.00, AAAAAAAAAAAA=0.00, AAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAA=0.00
Other Sub 476 AAAAAAAAAAA=1.000 AAAAAAA=0.000, AAAAAAAAAA=0.000, AAAAAAAAAAAA=0.000, AAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAA=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
Allele Frequency Aggregator Total Global 13900 (A)11=1.00000 del(A)4=0.00000, delA=0.00000, dupA=0.00000, dupAA=0.00000, dupAAA=0.00000
Allele Frequency Aggregator European Sub 9648 (A)11=1.0000 del(A)4=0.0000, delA=0.0000, dupA=0.0000, dupAA=0.0000, dupAAA=0.0000
Allele Frequency Aggregator African Sub 2834 (A)11=1.0000 del(A)4=0.0000, delA=0.0000, dupA=0.0000, dupAA=0.0000, dupAAA=0.0000
Allele Frequency Aggregator Latin American 2 Sub 604 (A)11=1.000 del(A)4=0.000, delA=0.000, dupA=0.000, dupAA=0.000, dupAAA=0.000
Allele Frequency Aggregator Other Sub 476 (A)11=1.000 del(A)4=0.000, delA=0.000, dupA=0.000, dupAA=0.000, dupAAA=0.000
Allele Frequency Aggregator Latin American 1 Sub 144 (A)11=1.000 del(A)4=0.000, delA=0.000, dupA=0.000, dupAA=0.000, dupAAA=0.000
Allele Frequency Aggregator Asian Sub 110 (A)11=1.000 del(A)4=0.000, delA=0.000, dupA=0.000, dupAA=0.000, dupAAA=0.000
Allele Frequency Aggregator South Asian Sub 84 (A)11=1.00 del(A)4=0.00, delA=0.00, dupA=0.00, dupAA=0.00, dupAAA=0.00
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 (A)11=0.991 delA=0.009
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.p14 chr 16 NC_000016.10:g.56357279_56357282del
GRCh38.p14 chr 16 NC_000016.10:g.56357282del
GRCh38.p14 chr 16 NC_000016.10:g.56357282dup
GRCh38.p14 chr 16 NC_000016.10:g.56357281_56357282dup
GRCh38.p14 chr 16 NC_000016.10:g.56357280_56357282dup
GRCh37.p13 chr 16 NC_000016.9:g.56391191_56391194del
GRCh37.p13 chr 16 NC_000016.9:g.56391194del
GRCh37.p13 chr 16 NC_000016.9:g.56391194dup
GRCh37.p13 chr 16 NC_000016.9:g.56391193_56391194dup
GRCh37.p13 chr 16 NC_000016.9:g.56391192_56391194dup
GNAO1 RefSeqGene NG_042800.1:g.170941_170944del
GNAO1 RefSeqGene NG_042800.1:g.170944del
GNAO1 RefSeqGene NG_042800.1:g.170944dup
GNAO1 RefSeqGene NG_042800.1:g.170943_170944dup
GNAO1 RefSeqGene NG_042800.1:g.170942_170944dup
Gene: GNAO1, G protein subunit alpha o1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
GNAO1 transcript variant 1 NM_020988.3:c.*1198_*1208= N/A 3 Prime UTR Variant
GNAO1 transcript variant 2 NM_138736.3:c. N/A Genic Downstream Transcript Variant
GNAO1 transcript variant X2 XM_011523003.4:c.*1198_*1…

XM_011523003.4:c.*1198_*1208=

N/A 3 Prime UTR Variant
GNAO1 transcript variant X1 XR_007064866.1:n. N/A Genic Downstream 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
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 (A)11= del(A)4 delA dupA dupAA dupAAA
GRCh38.p14 chr 16 NC_000016.10:g.56357272_56357282= NC_000016.10:g.56357279_56357282del NC_000016.10:g.56357282del NC_000016.10:g.56357282dup NC_000016.10:g.56357281_56357282dup NC_000016.10:g.56357280_56357282dup
GRCh37.p13 chr 16 NC_000016.9:g.56391184_56391194= NC_000016.9:g.56391191_56391194del NC_000016.9:g.56391194del NC_000016.9:g.56391194dup NC_000016.9:g.56391193_56391194dup NC_000016.9:g.56391192_56391194dup
GNAO1 RefSeqGene NG_042800.1:g.170934_170944= NG_042800.1:g.170941_170944del NG_042800.1:g.170944del NG_042800.1:g.170944dup NG_042800.1:g.170943_170944dup NG_042800.1:g.170942_170944dup
GNAO1 transcript variant 1 NM_020988.3:c.*1198_*1208= NM_020988.3:c.*1205_*1208del NM_020988.3:c.*1208del NM_020988.3:c.*1208dup NM_020988.3:c.*1207_*1208dup NM_020988.3:c.*1206_*1208dup
GNAO1 transcript variant 1 NM_020988.2:c.*1198_*1208= NM_020988.2:c.*1205_*1208del NM_020988.2:c.*1208del NM_020988.2:c.*1208dup NM_020988.2:c.*1207_*1208dup NM_020988.2:c.*1206_*1208dup
GNAO1 transcript variant X2 XM_011523003.4:c.*1198_*1208= XM_011523003.4:c.*1205_*1208del XM_011523003.4:c.*1208del XM_011523003.4:c.*1208dup XM_011523003.4:c.*1207_*1208dup XM_011523003.4:c.*1206_*1208dup
GNAO1 transcript variant X1 XM_011523003.1:c.*1198_*1208= XM_011523003.1:c.*1205_*1208del XM_011523003.1:c.*1208del XM_011523003.1:c.*1208dup XM_011523003.1:c.*1207_*1208dup XM_011523003.1:c.*1206_*1208dup
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#.

21 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSMP ss664319165 Apr 01, 2015 (144)
2 SSIP ss947357075 Aug 21, 2014 (142)
3 EVA-GONL ss992521375 Aug 21, 2014 (142)
4 SWEGEN ss3014563741 Nov 08, 2017 (151)
5 BIOINF_KMB_FNS_UNIBA ss3645420566 Oct 12, 2018 (152)
6 EVA ss3834585849 Apr 27, 2020 (154)
7 GNOMAD ss4301532374 Apr 26, 2021 (155)
8 GNOMAD ss4301532375 Apr 26, 2021 (155)
9 GNOMAD ss4301532376 Apr 26, 2021 (155)
10 GNOMAD ss4301532377 Apr 26, 2021 (155)
11 TOMMO_GENOMICS ss5219712260 Apr 26, 2021 (155)
12 TOMMO_GENOMICS ss5219712261 Apr 26, 2021 (155)
13 1000G_HIGH_COVERAGE ss5301068189 Oct 16, 2022 (156)
14 HUGCELL_USP ss5494410209 Oct 16, 2022 (156)
15 HUGCELL_USP ss5494410211 Oct 16, 2022 (156)
16 HUGCELL_USP ss5494410212 Oct 16, 2022 (156)
17 SANFORD_IMAGENETICS ss5658966472 Oct 16, 2022 (156)
18 TOMMO_GENOMICS ss5774761595 Oct 16, 2022 (156)
19 TOMMO_GENOMICS ss5774761596 Oct 16, 2022 (156)
20 YY_MCH ss5816000512 Oct 16, 2022 (156)
21 EVA ss5851579158 Oct 16, 2022 (156)
22 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 490472806 (NC_000016.10:56357271::A 658/115698)
Row 490472807 (NC_000016.10:56357271::AA 1/115846)
Row 490472808 (NC_000016.10:56357271::AAA 90/115844)...

- Apr 26, 2021 (155)
23 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 490472806 (NC_000016.10:56357271::A 658/115698)
Row 490472807 (NC_000016.10:56357271::AA 1/115846)
Row 490472808 (NC_000016.10:56357271::AAA 90/115844)...

- Apr 26, 2021 (155)
24 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 490472806 (NC_000016.10:56357271::A 658/115698)
Row 490472807 (NC_000016.10:56357271::AA 1/115846)
Row 490472808 (NC_000016.10:56357271::AAA 90/115844)...

- Apr 26, 2021 (155)
25 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 490472806 (NC_000016.10:56357271::A 658/115698)
Row 490472807 (NC_000016.10:56357271::AA 1/115846)
Row 490472808 (NC_000016.10:56357271::AAA 90/115844)...

- Apr 26, 2021 (155)
26 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 490472806 (NC_000016.10:56357271::A 658/115698)
Row 490472807 (NC_000016.10:56357271::AA 1/115846)
Row 490472808 (NC_000016.10:56357271::AAA 90/115844)...

- Apr 26, 2021 (155)
27 Genome of the Netherlands Release 5 NC_000016.9 - 56391184 Apr 27, 2020 (154)
28 8.3KJPN

Submission ignored due to conflicting rows:
Row 77681567 (NC_000016.9:56391183::A 192/16760)
Row 77681568 (NC_000016.9:56391183:A: 6/16760)

- Apr 26, 2021 (155)
29 8.3KJPN

Submission ignored due to conflicting rows:
Row 77681567 (NC_000016.9:56391183::A 192/16760)
Row 77681568 (NC_000016.9:56391183:A: 6/16760)

- Apr 26, 2021 (155)
30 14KJPN

Submission ignored due to conflicting rows:
Row 108598699 (NC_000016.10:56357271:A: 11/28244)
Row 108598700 (NC_000016.10:56357271::A 296/28244)

- Oct 16, 2022 (156)
31 14KJPN

Submission ignored due to conflicting rows:
Row 108598699 (NC_000016.10:56357271:A: 11/28244)
Row 108598700 (NC_000016.10:56357271::A 296/28244)

- Oct 16, 2022 (156)
32 ALFA NC_000016.10 - 56357272 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
ss4301532377, ss5301068189 NC_000016.10:56357271:AAAA: NC_000016.10:56357271:AAAAAAAAAAA:…

NC_000016.10:56357271:AAAAAAAAAAA:AAAAAAA

(self)
761594383 NC_000016.10:56357271:AAAAAAAAAAA:…

NC_000016.10:56357271:AAAAAAAAAAA:AAAAAAA

NC_000016.10:56357271:AAAAAAAAAAA:…

NC_000016.10:56357271:AAAAAAAAAAA:AAAAAAA

(self)
17200859, ss992521375, ss3014563741, ss5219712261 NC_000016.9:56391183:A: NC_000016.10:56357271:AAAAAAAAAAA:…

NC_000016.10:56357271:AAAAAAAAAAA:AAAAAAAAAA

(self)
ss5494410211, ss5774761595 NC_000016.10:56357271:A: NC_000016.10:56357271:AAAAAAAAAAA:…

NC_000016.10:56357271:AAAAAAAAAAA:AAAAAAAAAA

(self)
761594383 NC_000016.10:56357271:AAAAAAAAAAA:…

NC_000016.10:56357271:AAAAAAAAAAA:AAAAAAAAAA

NC_000016.10:56357271:AAAAAAAAAAA:…

NC_000016.10:56357271:AAAAAAAAAAA:AAAAAAAAAA

(self)
ss664319165, ss947357075, ss3834585849, ss5219712260, ss5658966472 NC_000016.9:56391183::A NC_000016.10:56357271:AAAAAAAAAAA:…

NC_000016.10:56357271:AAAAAAAAAAA:AAAAAAAAAAAA

(self)
ss3645420566, ss4301532374, ss5494410209, ss5774761596, ss5816000512, ss5851579158 NC_000016.10:56357271::A NC_000016.10:56357271:AAAAAAAAAAA:…

NC_000016.10:56357271:AAAAAAAAAAA:AAAAAAAAAAAA

(self)
761594383 NC_000016.10:56357271:AAAAAAAAAAA:…

NC_000016.10:56357271:AAAAAAAAAAA:AAAAAAAAAAAA

NC_000016.10:56357271:AAAAAAAAAAA:…

NC_000016.10:56357271:AAAAAAAAAAA:AAAAAAAAAAAA

(self)
ss4301532375 NC_000016.10:56357271::AA NC_000016.10:56357271:AAAAAAAAAAA:…

NC_000016.10:56357271:AAAAAAAAAAA:AAAAAAAAAAAAA

(self)
761594383 NC_000016.10:56357271:AAAAAAAAAAA:…

NC_000016.10:56357271:AAAAAAAAAAA:AAAAAAAAAAAAA

NC_000016.10:56357271:AAAAAAAAAAA:…

NC_000016.10:56357271:AAAAAAAAAAA:AAAAAAAAAAAAA

(self)
ss4301532376, ss5494410212 NC_000016.10:56357271::AAA NC_000016.10:56357271:AAAAAAAAAAA:…

NC_000016.10:56357271:AAAAAAAAAAA:AAAAAAAAAAAAAA

(self)
761594383 NC_000016.10:56357271:AAAAAAAAAAA:…

NC_000016.10:56357271:AAAAAAAAAAA:AAAAAAAAAAAAAA

NC_000016.10:56357271:AAAAAAAAAAA:…

NC_000016.10:56357271:AAAAAAAAAAA:AAAAAAAAAAAAAA

(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 rs540514958

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.post761+d5e8e07