Name: rs1345557258
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.

rs1345557258

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:23747437-23747446 (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: delCA / dupCA
Variation Type: Indel Insertion and Deletion
Frequency: delCA=0.000007 (1/139814, GnomAD)
delCA=0.00005 (1/18520, ALFA)
delCA=0.0002 (1/4480, Estonian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ATAD2B : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	HTRZ	HWEP
Total	Global	18520	CACACACACA=0.99995	CACACACA=0.00005, CACACACACACA=0.00000	0.999892	0.000108	0
European	Sub	14152	CACACACACA=0.99993	CACACACA=0.00007, CACACACACACA=0.00000	0.999859	0.000141	0
African	Sub	2898	CACACACACA=1.0000	CACACACA=0.0000, CACACACACACA=0.0000	1.0	0.0	N/A
African Others	Sub	114	CACACACACA=1.000	CACACACA=0.000, CACACACACACA=0.000	1.0	0.0	N/A
African American	Sub	2784	CACACACACA=1.0000	CACACACA=0.0000, CACACACACACA=0.0000	1.0	0.0	N/A
Asian	Sub	112	CACACACACA=1.000	CACACACA=0.000, CACACACACACA=0.000	1.0	0.0	N/A
East Asian	Sub	86	CACACACACA=1.00	CACACACA=0.00, CACACACACACA=0.00	1.0	0.0	N/A
Other Asian	Sub	26	CACACACACA=1.00	CACACACA=0.00, CACACACACACA=0.00	1.0	0.0	N/A
Latin American 1	Sub	146	CACACACACA=1.000	CACACACA=0.000, CACACACACACA=0.000	1.0	0.0	N/A
Latin American 2	Sub	610	CACACACACA=1.000	CACACACA=0.000, CACACACACACA=0.000	1.0	0.0	N/A
South Asian	Sub	98	CACACACACA=1.00	CACACACA=0.00, CACACACACACA=0.00	1.0	0.0	N/A
Other	Sub	504	CACACACACA=1.000	CACACACA=0.000, CACACACACACA=0.000	1.0	0.0	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
gnomAD - Genomes	Global	Study-wide	139814	(CA)₅=0.999993	delCA=0.000007
gnomAD - Genomes	European	Sub	75756	(CA)₅=0.99999	delCA=0.00001
gnomAD - Genomes	African	Sub	41882	(CA)₅=1.00000	delCA=0.00000
gnomAD - Genomes	American	Sub	13580	(CA)₅=1.00000	delCA=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	(CA)₅=1.0000	delCA=0.0000
gnomAD - Genomes	East Asian	Sub	3130	(CA)₅=1.0000	delCA=0.0000
gnomAD - Genomes	Other	Sub	2144	(CA)₅=1.0000	delCA=0.0000
Allele Frequency Aggregator	Total	Global	18520	(CA)₅=0.99995	delCA=0.00005, dupCA=0.00000
Allele Frequency Aggregator	European	Sub	14152	(CA)₅=0.99993	delCA=0.00007, dupCA=0.00000
Allele Frequency Aggregator	African	Sub	2898	(CA)₅=1.0000	delCA=0.0000, dupCA=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	(CA)₅=1.000	delCA=0.000, dupCA=0.000
Allele Frequency Aggregator	Other	Sub	504	(CA)₅=1.000	delCA=0.000, dupCA=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	(CA)₅=1.000	delCA=0.000, dupCA=0.000
Allele Frequency Aggregator	Asian	Sub	112	(CA)₅=1.000	delCA=0.000, dupCA=0.000
Allele Frequency Aggregator	South Asian	Sub	98	(CA)₅=1.00	delCA=0.00, dupCA=0.00
Genetic variation in the Estonian population	Estonian	Study-wide	4480	(CA)₅=0.9998	delCA=0.0002

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 2	NC_000002.12:g.23747437CA[4]
GRCh38.p14 chr 2	NC_000002.12:g.23747437CA[6]
GRCh37.p13 chr 2	NC_000002.11:g.23970307CA[4]
GRCh37.p13 chr 2	NC_000002.11:g.23970307CA[6]
ATAD2B RefSeqGene	NG_029017.2:g.184621TG[4]
ATAD2B RefSeqGene	NG_029017.2:g.184621TG[6]

Gene: ATAD2B, ATPase family AAA domain containing 2B (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ATAD2B transcript variant 2	NM_001242338.3:c.	N/A	Genic Downstream Transcript Variant
ATAD2B transcript variant 4	NM_001354107.2:c.	N/A	Genic Downstream Transcript Variant
ATAD2B transcript variant 1	NM_017552.4:c.	N/A	Genic Downstream Transcript Variant
ATAD2B transcript variant 3	NR_125717.2:n.	N/A	Genic Downstream Transcript Variant
ATAD2B transcript variant X7	XM_006712030.5:c.4377+673… XM_006712030.5:c.4377+6733TG[4]	N/A	Intron Variant
ATAD2B transcript variant X2	XM_011532918.4:c.4377+673… XM_011532918.4:c.4377+6733TG[4]	N/A	Intron Variant
ATAD2B transcript variant X3	XM_011532919.4:c.4362+673… XM_011532919.4:c.4362+6733TG[4]	N/A	Intron Variant
ATAD2B transcript variant X4	XM_011532920.4:c.4335+673… XM_011532920.4:c.4335+6733TG[4]	N/A	Intron Variant
ATAD2B transcript variant X1	XM_047444799.1:c.4320+673… XM_047444799.1:c.4320+6733TG[4]	N/A	Intron Variant
ATAD2B transcript variant X5	XM_005264372.5:c.	N/A	Genic Downstream Transcript Variant
ATAD2B transcript variant X10	XM_006712031.5:c.	N/A	Genic Downstream Transcript Variant
ATAD2B transcript variant X8	XM_011532924.4:c.	N/A	Genic Downstream Transcript Variant
ATAD2B transcript variant X9	XM_011532925.4:c.	N/A	Genic Downstream Transcript Variant
ATAD2B transcript variant X16	XM_011532928.3:c.	N/A	Genic Downstream Transcript Variant
ATAD2B transcript variant X18	XM_011532929.4:c.	N/A	Genic Downstream Transcript Variant
ATAD2B transcript variant X19	XM_011532930.4:c.	N/A	Genic Downstream Transcript Variant
ATAD2B transcript variant X20	XM_011532931.4:c.	N/A	Genic Downstream Transcript Variant
ATAD2B transcript variant X22	XM_011532932.3:c.	N/A	Genic Downstream Transcript Variant
ATAD2B transcript variant X11	XM_047444800.1:c.	N/A	Genic Downstream Transcript Variant
ATAD2B transcript variant X12	XM_047444801.1:c.	N/A	Genic Downstream Transcript Variant
ATAD2B transcript variant X13	XM_047444802.1:c.	N/A	Genic Downstream Transcript Variant
ATAD2B transcript variant X15	XM_047444803.1:c.	N/A	Genic Downstream Transcript Variant
ATAD2B transcript variant X17	XM_047444804.1:c.	N/A	Genic Downstream Transcript Variant
ATAD2B transcript variant X21	XM_047444805.1:c.	N/A	Genic Downstream Transcript Variant
ATAD2B transcript variant X23	XM_047444806.1:c.	N/A	Genic Downstream Transcript Variant
ATAD2B transcript variant X24	XM_047444807.1:c.	N/A	Genic Downstream Transcript Variant
ATAD2B transcript variant X25	XM_047444808.1:c.	N/A	Genic Downstream Transcript Variant
ATAD2B transcript variant X6	XR_001738780.3:n.	N/A	Intron Variant
ATAD2B transcript variant X14	XR_001738782.3:n.	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	(CA)₅=	delCA	dupCA
GRCh38.p14 chr 2	NC_000002.12:g.23747437_23747446=	NC_000002.12:g.23747437CA[4]	NC_000002.12:g.23747437CA[6]
GRCh37.p13 chr 2	NC_000002.11:g.23970307_23970316=	NC_000002.11:g.23970307CA[4]	NC_000002.11:g.23970307CA[6]
ATAD2B RefSeqGene	NG_029017.2:g.184621_184630=	NG_029017.2:g.184621TG[4]	NG_029017.2:g.184621TG[6]
ATAD2B transcript variant X7	XM_006712030.5:c.4377+6742=	XM_006712030.5:c.4377+6733TG[4]	XM_006712030.5:c.4377+6733TG[6]
ATAD2B transcript variant X2	XM_011532918.4:c.4377+6742=	XM_011532918.4:c.4377+6733TG[4]	XM_011532918.4:c.4377+6733TG[6]
ATAD2B transcript variant X3	XM_011532919.4:c.4362+6742=	XM_011532919.4:c.4362+6733TG[4]	XM_011532919.4:c.4362+6733TG[6]
ATAD2B transcript variant X4	XM_011532920.4:c.4335+6742=	XM_011532920.4:c.4335+6733TG[4]	XM_011532920.4:c.4335+6733TG[6]
ATAD2B transcript variant X1	XM_047444799.1:c.4320+6742=	XM_047444799.1:c.4320+6733TG[4]	XM_047444799.1:c.4320+6733TG[6]

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#.

2 SubSNP, 3 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss2770809834	Jan 10, 2018 (151)
2	EGCUT_WGS	ss3657087742	Jul 12, 2019 (153)
3	Genetic variation in the Estonian population	NC_000002.11 - 23970307	Oct 11, 2018 (152)
4	gnomAD - Genomes	NC_000002.12 - 23747437	Apr 26, 2021 (155)
5	ALFA	NC_000002.12 - 23747437	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
2825990, ss2770809834, ss3657087742	NC_000002.11:23970306:CA:	NC_000002.12:23747436:CACACACACA:C… NC_000002.12:23747436:CACACACACA:CACACACA	(self)
51222001	NC_000002.12:23747436:CA:	NC_000002.12:23747436:CACACACACA:C… NC_000002.12:23747436:CACACACACA:CACACACA	(self)
7520719771	NC_000002.12:23747436:CACACACACA:C… NC_000002.12:23747436:CACACACACA:CACACACA	NC_000002.12:23747436:CACACACACA:C… NC_000002.12:23747436:CACACACACA:CACACACA	(self)
7520719771	NC_000002.12:23747436:CACACACACA:C… NC_000002.12:23747436:CACACACACA:CACACACACACA	NC_000002.12:23747436:CACACACACA:C… NC_000002.12:23747436:CACACACACA:CACACACACACA	(self)

Removed from this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Destination RSIDs
187983573, ss3301771466	NC_000002.12:23747436::CA	NC_000002.12:23747436:CACACACACA:C… NC_000002.12:23747436:CACACACACA:CACACACACACA

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs1345557258

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

rs1345557258