Name: rs557085512
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.

rs557085512

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:24888670 (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: A>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.000314 (83/264690, TOPMED)
G=0.000342 (48/140284, GnomAD)
G=0.00000 (0/14050, ALFA) (+ 2 more)
G=0.0003 (2/6404, 1000G_30x)
G=0.0004 (2/5008, 1000G)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CENPJ : Intron Variant
RNF17 : 500B Downstream 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	14050	A=1.00000	G=0.00000
European	Sub	9690	A=1.0000	G=0.0000
African	Sub	2898	A=1.0000	G=0.0000
African Others	Sub	114	A=1.000	G=0.000
African American	Sub	2784	A=1.0000	G=0.0000
Asian	Sub	112	A=1.000	G=0.000
East Asian	Sub	86	A=1.00	G=0.00
Other Asian	Sub	26	A=1.00	G=0.00
Latin American 1	Sub	146	A=1.000	G=0.000
Latin American 2	Sub	610	A=1.000	G=0.000
South Asian	Sub	98	A=1.00	G=0.00
Other	Sub	496	A=1.000	G=0.000

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	A=0.999686	G=0.000314
gnomAD - Genomes	Global	Study-wide	140284	A=0.999658	G=0.000342
gnomAD - Genomes	European	Sub	75954	A=1.00000	G=0.00000
gnomAD - Genomes	African	Sub	42058	A=0.99891	G=0.00109
gnomAD - Genomes	American	Sub	13662	A=0.99993	G=0.00007
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	A=1.0000	G=0.0000
gnomAD - Genomes	East Asian	Sub	3134	A=1.0000	G=0.0000
gnomAD - Genomes	Other	Sub	2154	A=0.9995	G=0.0005
Allele Frequency Aggregator	Total	Global	14050	A=1.00000	G=0.00000
Allele Frequency Aggregator	European	Sub	9690	A=1.0000	G=0.0000
Allele Frequency Aggregator	African	Sub	2898	A=1.0000	G=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	A=1.000	G=0.000
Allele Frequency Aggregator	Other	Sub	496	A=1.000	G=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	A=1.000	G=0.000
Allele Frequency Aggregator	Asian	Sub	112	A=1.000	G=0.000
Allele Frequency Aggregator	South Asian	Sub	98	A=1.00	G=0.00
1000Genomes_30x	Global	Study-wide	6404	A=0.9997	G=0.0003
1000Genomes_30x	African	Sub	1786	A=0.9994	G=0.0006
1000Genomes_30x	Europe	Sub	1266	A=1.0000	G=0.0000
1000Genomes_30x	South Asian	Sub	1202	A=0.9992	G=0.0008
1000Genomes_30x	East Asian	Sub	1170	A=1.0000	G=0.0000
1000Genomes_30x	American	Sub	980	A=1.000	G=0.000
1000Genomes	Global	Study-wide	5008	A=0.9996	G=0.0004
1000Genomes	African	Sub	1322	A=0.9992	G=0.0008
1000Genomes	East Asian	Sub	1008	A=1.0000	G=0.0000
1000Genomes	Europe	Sub	1006	A=1.0000	G=0.0000
1000Genomes	South Asian	Sub	978	A=0.999	G=0.001
1000Genomes	American	Sub	694	A=1.000	G=0.000

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 13	NC_000013.11:g.24888670A>G
GRCh37.p13 chr 13	NC_000013.10:g.25462808A>G
CENPJ RefSeqGene	NG_009165.2:g.39278T>C

Gene: CENPJ, centromere protein J (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CENPJ transcript variant 1	NM_018451.5:c.3301+646T>C	N/A	Intron Variant
CENPJ transcript variant 2	NR_047594.2:n.	N/A	Intron Variant
CENPJ transcript variant 3	NR_047595.2:n.	N/A	Intron Variant
CENPJ transcript variant X4	XM_011535149.3:c.3301+646… XM_011535149.3:c.3301+646T>C	N/A	Intron Variant
CENPJ transcript variant X1	XM_047430482.1:c.3301+646… XM_047430482.1:c.3301+646T>C	N/A	Intron Variant
CENPJ transcript variant X1	XM_047430483.1:c.3301+646… XM_047430483.1:c.3301+646T>C	N/A	Intron Variant
CENPJ transcript variant X3	XM_047430484.1:c.3301+646… XM_047430484.1:c.3301+646T>C	N/A	Intron Variant
CENPJ transcript variant X5	XM_011535150.3:c.	N/A	Genic Downstream Transcript Variant
CENPJ transcript variant X7	XM_017020673.2:c.	N/A	Genic Downstream Transcript Variant
CENPJ transcript variant X8	XM_047430485.1:c.	N/A	Genic Downstream Transcript Variant
CENPJ transcript variant X2	XR_941627.2:n.	N/A	Intron Variant
CENPJ transcript variant X6	XR_941628.2:n.	N/A	Genic Downstream Transcript Variant

Gene: RNF17, ring finger protein 17 (plus strand) : 500B Downstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
RNF17 transcript variant 2	NM_001184993.2:c.	N/A	N/A
RNF17 transcript variant 1	NM_031277.3:c.	N/A	N/A
RNF17 transcript variant X2	XM_011535156.3:c.	N/A	Downstream Transcript Variant
RNF17 transcript variant X5	XM_006719846.4:c.	N/A	N/A
RNF17 transcript variant X6	XM_006719849.3:c.	N/A	N/A
RNF17 transcript variant X1	XM_011535152.3:c.	N/A	N/A
RNF17 transcript variant X3	XM_011535155.3:c.	N/A	N/A
RNF17 transcript variant X4	XM_011535157.3:c.	N/A	N/A
RNF17 transcript variant X7	XM_011535158.3:c.	N/A	N/A
RNF17 transcript variant X8	XM_011535159.3:c.	N/A	N/A
RNF17 transcript variant X9	XM_011535160.3:c.	N/A	N/A
RNF17 transcript variant X12	XM_011535162.2:c.	N/A	N/A
RNF17 transcript variant X13	XM_011535163.2:c.	N/A	N/A
RNF17 transcript variant X14	XM_011535164.3:c.	N/A	N/A
RNF17 transcript variant X10	XM_017020676.2:c.	N/A	N/A
RNF17 transcript variant X15	XM_047430486.1:c.	N/A	N/A
RNF17 transcript variant X11	XM_047430488.1:c.	N/A	N/A

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	A=	G
GRCh38.p14 chr 13	NC_000013.11:g.24888670=	NC_000013.11:g.24888670A>G
GRCh37.p13 chr 13	NC_000013.10:g.25462808=	NC_000013.10:g.25462808A>G
CENPJ RefSeqGene	NG_009165.2:g.39278=	NG_009165.2:g.39278T>C
CENPJ transcript variant 1	NM_018451.4:c.3301+646=	NM_018451.4:c.3301+646T>C
CENPJ transcript variant 1	NM_018451.5:c.3301+646=	NM_018451.5:c.3301+646T>C
CENPJ transcript variant X4	XM_011535149.3:c.3301+646=	XM_011535149.3:c.3301+646T>C
CENPJ transcript variant X1	XM_047430482.1:c.3301+646=	XM_047430482.1:c.3301+646T>C
CENPJ transcript variant X1	XM_047430483.1:c.3301+646=	XM_047430483.1:c.3301+646T>C
CENPJ transcript variant X3	XM_047430484.1:c.3301+646=	XM_047430484.1:c.3301+646T>C

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#.

8 SubSNP, 5 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss1347508640	Aug 21, 2014 (142)
2	HUMAN_LONGEVITY	ss2194882324	Dec 20, 2016 (150)
3	GNOMAD	ss2917637946	Nov 08, 2017 (151)
4	TOPMED	ss4940063484	Apr 26, 2021 (155)
5	1000G_HIGH_COVERAGE	ss5293109315	Oct 16, 2022 (156)
6	EVA	ss5409629586	Oct 16, 2022 (156)
7	1000G_HIGH_COVERAGE	ss5591749583	Oct 16, 2022 (156)
8	EVA	ss5924384175	Oct 16, 2022 (156)
9	1000Genomes	NC_000013.10 - 25462808	Oct 12, 2018 (152)
10	1000Genomes_30x	NC_000013.11 - 24888670	Oct 16, 2022 (156)
11	gnomAD - Genomes	NC_000013.11 - 24888670	Apr 26, 2021 (155)
12	TopMed	NC_000013.11 - 24888670	Apr 26, 2021 (155)
13	ALFA	NC_000013.11 - 24888670	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
60352589, ss1347508640, ss2917637946, ss5409629586	NC_000013.10:25462807:A:G	NC_000013.11:24888669:A:G	(self)
79275518, 425607084, 155609142, 1597897583, ss2194882324, ss4940063484, ss5293109315, ss5591749583, ss5924384175	NC_000013.11:24888669:A:G	NC_000013.11:24888669:A:G	(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 rs557085512

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs557085512