Name: rs538255846
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.

rs538255846

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:24884111-24884116 (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: delTT
Variation Type: Indel Insertion and Deletion
Frequency: delTT=0.000196 (49/250188, GnomAD_exome)
delTT=0.000143 (19/133112, GnomAD)
delTT=0.000124 (15/120840, ExAC) (+ 3 more)
delTT=0.00010 (2/20850, ALFA)
delTT=0.0009 (6/6404, 1000G_30x)
delTT=0.0010 (5/5008, 1000G)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CENPJ : Intron Variant
RNF17 : Intron 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	20850	TTTTTT=0.99990	TTTT=0.00010
European	Sub	13680	TTTTTT=1.00000	TTTT=0.00000
African	Sub	3410	TTTTTT=0.9997	TTTT=0.0003
African Others	Sub	116	TTTTTT=1.000	TTTT=0.000
African American	Sub	3294	TTTTTT=0.9997	TTTT=0.0003
Asian	Sub	164	TTTTTT=1.000	TTTT=0.000
East Asian	Sub	110	TTTTTT=1.000	TTTT=0.000
Other Asian	Sub	54	TTTTTT=1.00	TTTT=0.00
Latin American 1	Sub	146	TTTTTT=1.000	TTTT=0.000
Latin American 2	Sub	610	TTTTTT=1.000	TTTT=0.000
South Asian	Sub	94	TTTTTT=1.00	TTTT=0.00
Other	Sub	2746	TTTTTT=0.9996	TTTT=0.0004

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
gnomAD - Exomes	Global	Study-wide	250188	(T)₆=0.999804	delTT=0.000196
gnomAD - Exomes	European	Sub	134522	(T)₆=0.999926	delTT=0.000074
gnomAD - Exomes	Asian	Sub	48892	(T)₆=1.00000	delTT=0.00000
gnomAD - Exomes	American	Sub	34384	(T)₆=0.99904	delTT=0.00096
gnomAD - Exomes	African	Sub	16226	(T)₆=1.00000	delTT=0.00000
gnomAD - Exomes	Ashkenazi Jewish	Sub	10062	(T)₆=0.99990	delTT=0.00010
gnomAD - Exomes	Other	Sub	6102	(T)₆=0.9992	delTT=0.0008
gnomAD - Genomes	Global	Study-wide	133112	(T)₆=0.999857	delTT=0.000143
gnomAD - Genomes	European	Sub	71666	(T)₆=0.99997	delTT=0.00003
gnomAD - Genomes	African	Sub	41134	(T)₆=1.00000	delTT=0.00000
gnomAD - Genomes	American	Sub	12168	(T)₆=0.99869	delTT=0.00131
gnomAD - Genomes	Ashkenazi Jewish	Sub	3122	(T)₆=1.0000	delTT=0.0000
gnomAD - Genomes	East Asian	Sub	2982	(T)₆=1.0000	delTT=0.0000
gnomAD - Genomes	Other	Sub	2040	(T)₆=0.9995	delTT=0.0005
ExAC	Global	Study-wide	120840	(T)₆=0.999876	delTT=0.000124
ExAC	Europe	Sub	73008	(T)₆=0.99993	delTT=0.00007
ExAC	Asian	Sub	25064	(T)₆=1.00000	delTT=0.00000
ExAC	American	Sub	11492	(T)₆=0.99913	delTT=0.00087
ExAC	African	Sub	10374	(T)₆=1.00000	delTT=0.00000
ExAC	Other	Sub	902	(T)₆=1.000	delTT=0.000
Allele Frequency Aggregator	Total	Global	20850	(T)₆=0.99990	delTT=0.00010
Allele Frequency Aggregator	European	Sub	13680	(T)₆=1.00000	delTT=0.00000
Allele Frequency Aggregator	African	Sub	3410	(T)₆=0.9997	delTT=0.0003
Allele Frequency Aggregator	Other	Sub	2746	(T)₆=0.9996	delTT=0.0004
Allele Frequency Aggregator	Latin American 2	Sub	610	(T)₆=1.000	delTT=0.000
Allele Frequency Aggregator	Asian	Sub	164	(T)₆=1.000	delTT=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	(T)₆=1.000	delTT=0.000
Allele Frequency Aggregator	South Asian	Sub	94	(T)₆=1.00	delTT=0.00
1000Genomes_30x	Global	Study-wide	6404	(T)₆=0.9991	delTT=0.0009
1000Genomes_30x	African	Sub	1786	(T)₆=1.0000	delTT=0.0000
1000Genomes_30x	Europe	Sub	1266	(T)₆=0.9992	delTT=0.0008
1000Genomes_30x	South Asian	Sub	1202	(T)₆=1.0000	delTT=0.0000
1000Genomes_30x	East Asian	Sub	1170	(T)₆=1.0000	delTT=0.0000
1000Genomes_30x	American	Sub	980	(T)₆=0.995	delTT=0.005
1000Genomes	Global	Study-wide	5008	(T)₆=0.9990	delTT=0.0010
1000Genomes	African	Sub	1322	(T)₆=1.0000	delTT=0.0000
1000Genomes	East Asian	Sub	1008	(T)₆=1.0000	delTT=0.0000
1000Genomes	Europe	Sub	1006	(T)₆=0.9990	delTT=0.0010
1000Genomes	South Asian	Sub	978	(T)₆=1.000	delTT=0.000
1000Genomes	American	Sub	694	(T)₆=0.994	delTT=0.006

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.24884115_24884116del
GRCh37.p13 chr 13	NC_000013.10:g.25458253_25458254del
CENPJ RefSeqGene	NG_009165.2:g.43836_43837del

Gene: CENPJ, centromere protein J (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CENPJ transcript variant 1	NM_018451.5:c.3704-29_370… NM_018451.5:c.3704-29_3704-28del	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 X1	XM_047430482.1:c.3704-29_… XM_047430482.1:c.3704-29_3704-28del	N/A	Intron Variant
CENPJ transcript variant X1	XM_047430483.1:c.3704-29_… XM_047430483.1:c.3704-29_3704-28del	N/A	Intron Variant
CENPJ transcript variant X4	XM_011535149.3:c.	N/A	Genic Downstream Transcript 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 X3	XM_047430484.1: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	Genic Downstream Transcript Variant
CENPJ transcript variant X6	XR_941628.2:n.	N/A	Genic Downstream Transcript Variant

Gene: RNF17, ring finger protein 17 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RNF17 transcript variant 2	NM_001184993.2:c.	N/A	Genic Downstream Transcript Variant
RNF17 transcript variant 1	NM_031277.3:c.	N/A	Genic Downstream Transcript Variant
RNF17 transcript variant X2	XM_011535156.3:c.11-3999… XM_011535156.3:c.11-3999_*11-3998del	N/A	Intron Variant
RNF17 transcript variant X5	XM_006719846.4:c.	N/A	Genic Downstream Transcript Variant
RNF17 transcript variant X6	XM_006719849.3:c.	N/A	Genic Downstream Transcript Variant
RNF17 transcript variant X1	XM_011535152.3:c.	N/A	Genic Downstream Transcript Variant
RNF17 transcript variant X3	XM_011535155.3:c.	N/A	Genic Downstream Transcript Variant
RNF17 transcript variant X4	XM_011535157.3:c.	N/A	Genic Downstream Transcript Variant
RNF17 transcript variant X7	XM_011535158.3:c.	N/A	Genic Downstream Transcript Variant
RNF17 transcript variant X8	XM_011535159.3:c.	N/A	Genic Downstream Transcript Variant
RNF17 transcript variant X9	XM_011535160.3:c.	N/A	Genic Downstream Transcript Variant
RNF17 transcript variant X12	XM_011535162.2:c.	N/A	Genic Downstream Transcript Variant
RNF17 transcript variant X13	XM_011535163.2:c.	N/A	Genic Downstream Transcript Variant
RNF17 transcript variant X14	XM_011535164.3:c.	N/A	Genic Downstream Transcript Variant
RNF17 transcript variant X10	XM_017020676.2:c.	N/A	Genic Downstream Transcript Variant
RNF17 transcript variant X15	XM_047430486.1:c.	N/A	Genic Downstream Transcript Variant
RNF17 transcript variant X11	XM_047430488.1:c.	N/A	Genic Downstream 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	(T)₆=	delTT
GRCh38.p14 chr 13	NC_000013.11:g.24884111_24884116=	NC_000013.11:g.24884115_24884116del
GRCh37.p13 chr 13	NC_000013.10:g.25458249_25458254=	NC_000013.10:g.25458253_25458254del
CENPJ RefSeqGene	NG_009165.2:g.43832_43837=	NG_009165.2:g.43836_43837del
CENPJ transcript variant 1	NM_018451.4:c.3704-28=	NM_018451.4:c.3704-29_3704-28del
CENPJ transcript variant 1	NM_018451.5:c.3704-28=	NM_018451.5:c.3704-29_3704-28del
RNF17 transcript variant X2	XM_011535156.3:c.*11-4003=	XM_011535156.3:c.11-3999_11-3998del
CENPJ transcript variant X1	XM_047430482.1:c.3704-28=	XM_047430482.1:c.3704-29_3704-28del
CENPJ transcript variant X1	XM_047430483.1:c.3704-28=	XM_047430483.1:c.3704-29_3704-28del

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#.

7 SubSNP, 6 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss1372921702	Aug 21, 2014 (142)
2	EVA_EXAC	ss1712033986	Apr 01, 2015 (144)
3	GNOMAD	ss2749020169	Nov 08, 2017 (151)
4	GNOMAD	ss2917637596	Nov 08, 2017 (151)
5	1000G_HIGH_COVERAGE	ss5293109216	Oct 16, 2022 (156)
6	HUGCELL_USP	ss5487534506	Oct 16, 2022 (156)
7	1000G_HIGH_COVERAGE	ss5591749429	Oct 16, 2022 (156)
8	1000Genomes	NC_000013.10 - 25458249	Oct 12, 2018 (152)
9	1000Genomes_30x	NC_000013.11 - 24884111	Oct 16, 2022 (156)
10	ExAC	NC_000013.10 - 25458249	Oct 12, 2018 (152)
11	gnomAD - Genomes	NC_000013.11 - 24884111	Apr 26, 2021 (155)
12	gnomAD - Exomes	NC_000013.10 - 25458249	Jul 13, 2019 (153)
13	ALFA	NC_000013.11 - 24884111	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
60352455, 1554707, 9563939, ss1372921702, ss1712033986, ss2749020169, ss2917637596	NC_000013.10:25458248:TT:	NC_000013.11:24884110:TTTTTT:TTTT	(self)
79275364, 425606179, ss5293109216, ss5487534506, ss5591749429	NC_000013.11:24884110:TT:	NC_000013.11:24884110:TTTTTT:TTTT	(self)
1596104287	NC_000013.11:24884110:TTTTTT:TTTT	NC_000013.11:24884110:TTTTTT:TTTT	(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 rs538255846

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs538255846