Name: rs1267606855
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.

rs1267606855

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:56393132-56393146 (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(CA)₃ / delCACA / delCA / dupCA…
del(CA)₃ / delCACA / delCA / dupCA / dupCACA
Variation Type: Indel Insertion and Deletion
Frequency: del(CA)₃=0.00000 (0/13992, ALFA)
delCACA=0.00000 (0/13992, ALFA)
delCA=0.00000 (0/13992, ALFA) (+ 3 more)
dupCA=0.00000 (0/13992, ALFA)
dupCACA=0.00000 (0/13992, ALFA)
dupCA=0.0382 (70/1832, Korea1K)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CSTF1 : Intron Variant
AURKA : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	HWEP
Total	Global	13992	ACACACACACACACA=1.00000	ACACACACA=0.00000, ACACACACACA=0.00000, ACACACACACACA=0.00000, ACACACACACACACACA=0.00000, ACACACACACACACACACA=0.00000	1.0	N/A
European	Sub	9686	ACACACACACACACA=1.0000	ACACACACA=0.0000, ACACACACACA=0.0000, ACACACACACACA=0.0000, ACACACACACACACACA=0.0000, ACACACACACACACACACA=0.0000	1.0	N/A
African	Sub	2860	ACACACACACACACA=1.0000	ACACACACA=0.0000, ACACACACACA=0.0000, ACACACACACACA=0.0000, ACACACACACACACACA=0.0000, ACACACACACACACACACA=0.0000	1.0	N/A
African Others	Sub	114	ACACACACACACACA=1.000	ACACACACA=0.000, ACACACACACA=0.000, ACACACACACACA=0.000, ACACACACACACACACA=0.000, ACACACACACACACACACA=0.000	1.0	N/A
African American	Sub	2746	ACACACACACACACA=1.0000	ACACACACA=0.0000, ACACACACACA=0.0000, ACACACACACACA=0.0000, ACACACACACACACACA=0.0000, ACACACACACACACACACA=0.0000	1.0	N/A
Asian	Sub	108	ACACACACACACACA=1.000	ACACACACA=0.000, ACACACACACA=0.000, ACACACACACACA=0.000, ACACACACACACACACA=0.000, ACACACACACACACACACA=0.000	1.0	N/A
East Asian	Sub	82	ACACACACACACACA=1.00	ACACACACA=0.00, ACACACACACA=0.00, ACACACACACACA=0.00, ACACACACACACACACA=0.00, ACACACACACACACACACA=0.00	1.0	N/A
Other Asian	Sub	26	ACACACACACACACA=1.00	ACACACACA=0.00, ACACACACACA=0.00, ACACACACACACA=0.00, ACACACACACACACACA=0.00, ACACACACACACACACACA=0.00	1.0	N/A
Latin American 1	Sub	144	ACACACACACACACA=1.000	ACACACACA=0.000, ACACACACACA=0.000, ACACACACACACA=0.000, ACACACACACACACACA=0.000, ACACACACACACACACACA=0.000	1.0	N/A
Latin American 2	Sub	608	ACACACACACACACA=1.000	ACACACACA=0.000, ACACACACACA=0.000, ACACACACACACA=0.000, ACACACACACACACACA=0.000, ACACACACACACACACACA=0.000	1.0	N/A
South Asian	Sub	94	ACACACACACACACA=1.00	ACACACACA=0.00, ACACACACACA=0.00, ACACACACACACA=0.00, ACACACACACACACACA=0.00, ACACACACACACACACACA=0.00	1.0	N/A
Other	Sub	492	ACACACACACACACA=1.000	ACACACACA=0.000, ACACACACACA=0.000, ACACACACACACA=0.000, ACACACACACACACACA=0.000, ACACACACACACACACACA=0.000	1.0	N/A

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
Allele Frequency Aggregator	Total	Global	13992	(AC)₇A=1.00000	del(CA)₃=0.00000, delCACA=0.00000, delCA=0.00000, dupCA=0.00000, dupCACA=0.00000
Allele Frequency Aggregator	European	Sub	9686	(AC)₇A=1.0000	del(CA)₃=0.0000, delCACA=0.0000, delCA=0.0000, dupCA=0.0000, dupCACA=0.0000
Allele Frequency Aggregator	African	Sub	2860	(AC)₇A=1.0000	del(CA)₃=0.0000, delCACA=0.0000, delCA=0.0000, dupCA=0.0000, dupCACA=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	608	(AC)₇A=1.000	del(CA)₃=0.000, delCACA=0.000, delCA=0.000, dupCA=0.000, dupCACA=0.000
Allele Frequency Aggregator	Other	Sub	492	(AC)₇A=1.000	del(CA)₃=0.000, delCACA=0.000, delCA=0.000, dupCA=0.000, dupCACA=0.000
Allele Frequency Aggregator	Latin American 1	Sub	144	(AC)₇A=1.000	del(CA)₃=0.000, delCACA=0.000, delCA=0.000, dupCA=0.000, dupCACA=0.000
Allele Frequency Aggregator	Asian	Sub	108	(AC)₇A=1.000	del(CA)₃=0.000, delCACA=0.000, delCA=0.000, dupCA=0.000, dupCACA=0.000
Allele Frequency Aggregator	South Asian	Sub	94	(AC)₇A=1.00	del(CA)₃=0.00, delCACA=0.00, delCA=0.00, dupCA=0.00, dupCACA=0.00
Korean Genome Project	KOREAN	Study-wide	1832	- No frequency provided	dupCA=0.0382

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 20	NC_000020.11:g.56393133CA[4]
GRCh38.p14 chr 20	NC_000020.11:g.56393133CA[5]
GRCh38.p14 chr 20	NC_000020.11:g.56393133CA[6]
GRCh38.p14 chr 20	NC_000020.11:g.56393133CA[8]
GRCh38.p14 chr 20	NC_000020.11:g.56393133CA[9]
GRCh37.p13 chr 20	NC_000020.10:g.54968189CA[4]
GRCh37.p13 chr 20	NC_000020.10:g.54968189CA[5]
GRCh37.p13 chr 20	NC_000020.10:g.54968189CA[6]
GRCh37.p13 chr 20	NC_000020.10:g.54968189CA[8]
GRCh37.p13 chr 20	NC_000020.10:g.54968189CA[9]
AURKA RefSeqGene	NG_012133.1:g.4151GT[4]
AURKA RefSeqGene	NG_012133.1:g.4151GT[5]
AURKA RefSeqGene	NG_012133.1:g.4151GT[6]
AURKA RefSeqGene	NG_012133.1:g.4151GT[8]
AURKA RefSeqGene	NG_012133.1:g.4151GT[9]

Gene: CSTF1, cleavage stimulation factor subunit 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CSTF1 transcript variant 1	NM_001033521.2:c.-33+594A… NM_001033521.2:c.-33+594AC[4]	N/A	Intron Variant
CSTF1 transcript variant 3	NM_001033522.2:c.-33+317A… NM_001033522.2:c.-33+317AC[4]	N/A	Intron Variant
CSTF1 transcript variant 2	NM_001324.3:c.-33+419AC[4]	N/A	Intron Variant
CSTF1 transcript variant X1	XM_011528600.2:c.-33+393A… XM_011528600.2:c.-33+393AC[4]	N/A	Intron Variant

Gene: AURKA, aurora kinase A (minus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
AURKA transcript variant 7	NM_001323303.2:c.	N/A	Upstream Transcript Variant
AURKA transcript variant 8	NM_001323304.2:c.	N/A	Upstream Transcript Variant
AURKA transcript variant 9	NM_001323305.2:c.	N/A	Upstream Transcript Variant
AURKA transcript variant 2	NM_003600.4:c.	N/A	Upstream Transcript Variant
AURKA transcript variant 1	NM_198433.3:c.	N/A	Upstream Transcript Variant
AURKA transcript variant 3	NM_198434.3:c.	N/A	Upstream Transcript Variant
AURKA transcript variant 4	NM_198435.3:c.	N/A	Upstream Transcript Variant
AURKA transcript variant 5	NM_198436.3:c.	N/A	Upstream Transcript Variant
AURKA transcript variant 6	NM_198437.3:c.	N/A	Upstream Transcript Variant
AURKA transcript variant X1	XM_017028034.3:c.	N/A	Upstream Transcript Variant
AURKA transcript variant X4	XM_017028035.2:c.	N/A	Upstream Transcript Variant
AURKA transcript variant X2	XM_047440427.1:c.	N/A	Upstream Transcript Variant
AURKA transcript variant X3	XM_047440428.1:c.	N/A	Upstream Transcript Variant

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	(AC)₇A=	del(CA)₃	delCACA	delCA	dupCA	dupCACA
GRCh38.p14 chr 20	NC_000020.11:g.56393132_56393146=	NC_000020.11:g.56393133CA[4]	NC_000020.11:g.56393133CA[5]	NC_000020.11:g.56393133CA[6]	NC_000020.11:g.56393133CA[8]	NC_000020.11:g.56393133CA[9]
GRCh37.p13 chr 20	NC_000020.10:g.54968188_54968202=	NC_000020.10:g.54968189CA[4]	NC_000020.10:g.54968189CA[5]	NC_000020.10:g.54968189CA[6]	NC_000020.10:g.54968189CA[8]	NC_000020.10:g.54968189CA[9]
AURKA RefSeqGene	NG_012133.1:g.4150_4164=	NG_012133.1:g.4151GT[4]	NG_012133.1:g.4151GT[5]	NG_012133.1:g.4151GT[6]	NG_012133.1:g.4151GT[8]	NG_012133.1:g.4151GT[9]
CSTF1 transcript variant 1	NM_001033521.1:c.-33+594=	NM_001033521.1:c.-33+594AC[4]	NM_001033521.1:c.-33+594AC[5]	NM_001033521.1:c.-33+594AC[6]	NM_001033521.1:c.-33+594AC[8]	NM_001033521.1:c.-33+594AC[9]
CSTF1 transcript variant 1	NM_001033521.2:c.-33+594=	NM_001033521.2:c.-33+594AC[4]	NM_001033521.2:c.-33+594AC[5]	NM_001033521.2:c.-33+594AC[6]	NM_001033521.2:c.-33+594AC[8]	NM_001033521.2:c.-33+594AC[9]
CSTF1 transcript variant 3	NM_001033522.1:c.-33+317=	NM_001033522.1:c.-33+317AC[4]	NM_001033522.1:c.-33+317AC[5]	NM_001033522.1:c.-33+317AC[6]	NM_001033522.1:c.-33+317AC[8]	NM_001033522.1:c.-33+317AC[9]
CSTF1 transcript variant 3	NM_001033522.2:c.-33+317=	NM_001033522.2:c.-33+317AC[4]	NM_001033522.2:c.-33+317AC[5]	NM_001033522.2:c.-33+317AC[6]	NM_001033522.2:c.-33+317AC[8]	NM_001033522.2:c.-33+317AC[9]
CSTF1 transcript variant 2	NM_001324.2:c.-33+419=	NM_001324.2:c.-33+419AC[4]	NM_001324.2:c.-33+419AC[5]	NM_001324.2:c.-33+419AC[6]	NM_001324.2:c.-33+419AC[8]	NM_001324.2:c.-33+419AC[9]
CSTF1 transcript variant 2	NM_001324.3:c.-33+419=	NM_001324.3:c.-33+419AC[4]	NM_001324.3:c.-33+419AC[5]	NM_001324.3:c.-33+419AC[6]	NM_001324.3:c.-33+419AC[8]	NM_001324.3:c.-33+419AC[9]
CSTF1 transcript variant X1	XM_011528600.2:c.-33+393=	XM_011528600.2:c.-33+393AC[4]	XM_011528600.2:c.-33+393AC[5]	XM_011528600.2:c.-33+393AC[6]	XM_011528600.2:c.-33+393AC[8]	XM_011528600.2:c.-33+393AC[9]

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#.

24 SubSNP, 9 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HUMANGENOME_JCVI	ss95743750	Oct 12, 2018 (152)
2	SWEGEN	ss3018380623	Nov 08, 2017 (151)
3	MCHAISSO	ss3064002789	Nov 08, 2017 (151)
4	MCHAISSO	ss3064002790	Nov 08, 2017 (151)
5	MCHAISSO	ss3064002791	Nov 08, 2017 (151)
6	MCHAISSO	ss3064860461	Nov 08, 2017 (151)
7	MCHAISSO	ss3064860462	Nov 08, 2017 (151)
8	MCHAISSO	ss3064860463	Nov 08, 2017 (151)
9	MCHAISSO	ss3064860464	Nov 08, 2017 (151)
10	MCHAISSO	ss3065824722	Nov 08, 2017 (151)
11	MCHAISSO	ss3065824723	Nov 08, 2017 (151)
12	MCHAISSO	ss3065824724	Nov 08, 2017 (151)
13	EVA_DECODE	ss3707192782	Jul 13, 2019 (153)
14	KOGIC	ss3982528198	Apr 27, 2020 (154)
15	GNOMAD	ss4355515514	Apr 26, 2021 (155)
16	GNOMAD	ss4355515515	Apr 26, 2021 (155)
17	GNOMAD	ss4355515525	Apr 26, 2021 (155)
18	TOMMO_GENOMICS	ss5230206585	Apr 26, 2021 (155)
19	TOMMO_GENOMICS	ss5230206587	Apr 26, 2021 (155)
20	1000G_HIGH_COVERAGE	ss5309231767	Oct 16, 2022 (156)
21	HUGCELL_USP	ss5501468931	Oct 16, 2022 (156)
22	TOMMO_GENOMICS	ss5790181611	Oct 16, 2022 (156)
23	TOMMO_GENOMICS	ss5790181614	Oct 16, 2022 (156)
24	YY_MCH	ss5818150283	Oct 16, 2022 (156)
25	gnomAD - Genomes Submission ignored due to conflicting rows: Row 555358797 (NC_000020.11:56393131::AC 511/125040) Row 555358798 (NC_000020.11:56393131::ACAC 3/125056) Row 555358808 (NC_000020.11:56393131:ACAC: 1/125056)	-	Apr 26, 2021 (155)
26	gnomAD - Genomes Submission ignored due to conflicting rows: Row 555358797 (NC_000020.11:56393131::AC 511/125040) Row 555358798 (NC_000020.11:56393131::ACAC 3/125056) Row 555358808 (NC_000020.11:56393131:ACAC: 1/125056)	-	Apr 26, 2021 (155)
27	gnomAD - Genomes Submission ignored due to conflicting rows: Row 555358797 (NC_000020.11:56393131::AC 511/125040) Row 555358798 (NC_000020.11:56393131::ACAC 3/125056) Row 555358808 (NC_000020.11:56393131:ACAC: 1/125056)	-	Apr 26, 2021 (155)
28	Korean Genome Project	NC_000020.11 - 56393132	Apr 27, 2020 (154)
29	8.3KJPN Submission ignored due to conflicting rows: Row 88175892 (NC_000020.10:54968187::AC 828/16744) Row 88175894 (NC_000020.10:54968187:AC: 2/16744)	-	Apr 26, 2021 (155)
30	8.3KJPN Submission ignored due to conflicting rows: Row 88175892 (NC_000020.10:54968187::AC 828/16744) Row 88175894 (NC_000020.10:54968187:AC: 2/16744)	-	Apr 26, 2021 (155)
31	14KJPN Submission ignored due to conflicting rows: Row 124018715 (NC_000020.11:56393131::AC 1409/28258) Row 124018718 (NC_000020.11:56393131:AC: 2/28258)	-	Oct 16, 2022 (156)
32	14KJPN Submission ignored due to conflicting rows: Row 124018715 (NC_000020.11:56393131::AC 1409/28258) Row 124018718 (NC_000020.11:56393131:AC: 2/28258)	-	Oct 16, 2022 (156)
33	ALFA	NC_000020.11 - 56393132	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
5992384257	NC_000020.11:56393131:ACACACACACAC… NC_000020.11:56393131:ACACACACACACACA:ACACACACA	NC_000020.11:56393131:ACACACACACAC… NC_000020.11:56393131:ACACACACACACACA:ACACACACA	(self)
ss4355515525	NC_000020.11:56393131:ACAC:	NC_000020.11:56393131:ACACACACACAC… NC_000020.11:56393131:ACACACACACACACA:ACACACACACA	(self)
5992384257	NC_000020.11:56393131:ACACACACACAC… NC_000020.11:56393131:ACACACACACACACA:ACACACACACA	NC_000020.11:56393131:ACACACACACAC… NC_000020.11:56393131:ACACACACACACACA:ACACACACACA	(self)
ss5230206587	NC_000020.10:54968187:AC:	NC_000020.11:56393131:ACACACACACAC… NC_000020.11:56393131:ACACACACACACACA:ACACACACACACA	(self)
ss5790181614	NC_000020.11:56393131:AC:	NC_000020.11:56393131:ACACACACACAC… NC_000020.11:56393131:ACACACACACACACA:ACACACACACACA	(self)
5992384257	NC_000020.11:56393131:ACACACACACAC… NC_000020.11:56393131:ACACACACACACACA:ACACACACACACA	NC_000020.11:56393131:ACACACACACAC… NC_000020.11:56393131:ACACACACACACACA:ACACACACACACA	(self)
ss3018380623, ss5230206585	NC_000020.10:54968187::AC	NC_000020.11:56393131:ACACACACACAC… NC_000020.11:56393131:ACACACACACACACA:ACACACACACACACACA	(self)
38906199, ss3064002789, ss3064002790, ss3064002791, ss3064860461, ss3064860462, ss3064860463, ss3064860464, ss3065824722, ss3065824723, ss3065824724, ss3707192782, ss3982528198, ss4355515514, ss5309231767, ss5501468931, ss5790181611, ss5818150283	NC_000020.11:56393131::AC	NC_000020.11:56393131:ACACACACACAC… NC_000020.11:56393131:ACACACACACACACA:ACACACACACACACACA	(self)
5992384257	NC_000020.11:56393131:ACACACACACAC… NC_000020.11:56393131:ACACACACACACACA:ACACACACACACACACA	NC_000020.11:56393131:ACACACACACAC… NC_000020.11:56393131:ACACACACACACACA:ACACACACACACACACA	(self)
ss95743750	NT_011362.10:25164294::CA	NC_000020.11:56393131:ACACACACACAC… NC_000020.11:56393131:ACACACACACACACA:ACACACACACACACACA	(self)
ss4355515515	NC_000020.11:56393131::ACAC	NC_000020.11:56393131:ACACACACACAC… NC_000020.11:56393131:ACACACACACACACA:ACACACACACACACACACA	(self)
5992384257	NC_000020.11:56393131:ACACACACACAC… NC_000020.11:56393131:ACACACACACACACA:ACACACACACACACACACA	NC_000020.11:56393131:ACACACACACAC… NC_000020.11:56393131:ACACACACACACACA:ACACACACACACACACACA	(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 rs1267606855

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
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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

rs1267606855