Name: rs1491488457
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.

rs1491488457

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr11:8912198-8912199 (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
Variation Type: Deletion
Frequency: delCA=0.01098 (310/28222, 14KJPN)
delCA=0.01250 (262/20960, GnomAD)
delCA=0.08279 (982/11862, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: AKIP1 : Intron Variant
DENND2B : 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	HTRZ	HWEP
Total	Global	11862	CA=0.91721	=0.08279	0.834429	0.165571	26
European	Sub	7618	CA=0.9078	=0.0922	0.8157	0.1843	21
African	Sub	2816	CA=0.9652	=0.0348	0.930398	0.069602	1
African Others	Sub	108	CA=0.991	=0.009	0.981481	0.018519	0
African American	Sub	2708	CA=0.9642	=0.0358	0.92836	0.07164	1
Asian	Sub	108	CA=0.898	=0.102	0.796296	0.203704	0
East Asian	Sub	84	CA=0.89	=0.11	0.785714	0.214286	0
Other Asian	Sub	24	CA=0.92	=0.08	0.833333	0.166667	0
Latin American 1	Sub	146	CA=0.897	=0.103	0.794521	0.205479	1
Latin American 2	Sub	610	CA=0.836	=0.164	0.672131	0.327869	7
South Asian	Sub	94	CA=0.89	=0.11	0.787234	0.212766	0
Other	Sub	470	CA=0.902	=0.098	0.804255	0.195745	2

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
14KJPN	JAPANESE	Study-wide	28222	CA=0.98902	delCA=0.01098
gnomAD - Genomes	Global	Study-wide	20960	CA=0.98750	delCA=0.01250
gnomAD - Genomes	European	Sub	10390	CA=0.98316	delCA=0.01684
gnomAD - Genomes	African	Sub	7590	CA=0.9954	delCA=0.0046
gnomAD - Genomes	American	Sub	1664	CA=0.9820	delCA=0.0180
gnomAD - Genomes	Ashkenazi Jewish	Sub	536	CA=0.983	delCA=0.017
gnomAD - Genomes	East Asian	Sub	464	CA=0.983	delCA=0.017
gnomAD - Genomes	Other	Sub	316	CA=0.984	delCA=0.016
Allele Frequency Aggregator	Total	Global	11862	CA=0.91721	delCA=0.08279
Allele Frequency Aggregator	European	Sub	7618	CA=0.9078	delCA=0.0922
Allele Frequency Aggregator	African	Sub	2816	CA=0.9652	delCA=0.0348
Allele Frequency Aggregator	Latin American 2	Sub	610	CA=0.836	delCA=0.164
Allele Frequency Aggregator	Other	Sub	470	CA=0.902	delCA=0.098
Allele Frequency Aggregator	Latin American 1	Sub	146	CA=0.897	delCA=0.103
Allele Frequency Aggregator	Asian	Sub	108	CA=0.898	delCA=0.102
Allele Frequency Aggregator	South Asian	Sub	94	CA=0.89	delCA=0.11

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 11	NC_000011.10:g.8912198_8912199del
GRCh37.p13 chr 11	NC_000011.9:g.8933745_8933746del
DENND2B RefSeqGene	NG_029450.1:g.3753_3754del
AKIP1 RefSeqGene	NG_030417.1:g.6045_6046del

Gene: AKIP1, A-kinase interacting protein 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
AKIP1 transcript variant 2	NM_001206646.2:c.222+527_… NM_001206646.2:c.222+527_222+528del	N/A	Intron Variant
AKIP1 transcript variant 3	NM_001206647.2:c.223-255_… NM_001206647.2:c.223-255_223-254del	N/A	Intron Variant
AKIP1 transcript variant 4	NM_001206648.2:c.222+527_… NM_001206648.2:c.222+527_222+528del	N/A	Intron Variant
AKIP1 transcript variant 1	NM_020642.4:c.223-255_223… NM_020642.4:c.223-255_223-254del	N/A	Intron Variant
AKIP1 transcript variant 5	NR_045417.2:n.	N/A	Intron Variant
AKIP1 transcript variant 6	NR_045418.2:n.	N/A	Intron Variant
AKIP1 transcript variant X1	XM_017018011.2:c.223-255_… XM_017018011.2:c.223-255_223-254del	N/A	Intron Variant
AKIP1 transcript variant X2	XM_047427261.1:c.222+527_… XM_047427261.1:c.222+527_222+528del	N/A	Intron Variant

Gene: DENND2B, DENN domain containing 2B (minus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
DENND2B transcript variant 1	NM_005418.4:c.	N/A	Upstream Transcript Variant
DENND2B transcript variant 4	NM_001376495.1:c.	N/A	N/A
DENND2B transcript variant 5	NM_001376496.1:c.	N/A	N/A
DENND2B transcript variant 6	NM_001376497.1:c.	N/A	N/A
DENND2B transcript variant 7	NM_001376498.1:c.	N/A	N/A
DENND2B transcript variant 8	NM_001376499.1:c.	N/A	N/A
DENND2B transcript variant 9	NM_001376500.1:c.	N/A	N/A
DENND2B transcript variant 10	NM_001376501.1:c.	N/A	N/A
DENND2B transcript variant 11	NM_001376502.1:c.	N/A	N/A
DENND2B transcript variant 12	NM_001376503.1:c.	N/A	N/A
DENND2B transcript variant 13	NM_001376504.1:c.	N/A	N/A
DENND2B transcript variant 14	NM_001376505.1:c.	N/A	N/A
DENND2B transcript variant 15	NM_001376506.1:c.	N/A	N/A
DENND2B transcript variant 2	NM_139157.3:c.	N/A	N/A
DENND2B transcript variant 3	NM_213618.2:c.	N/A	N/A
DENND2B transcript variant 16	NR_164814.1:n.	N/A	N/A
DENND2B transcript variant 17	NR_164815.1:n.	N/A	N/A
DENND2B transcript variant 18	NR_164816.1:n.	N/A	N/A
DENND2B transcript variant 19	NR_164817.1:n.	N/A	N/A
DENND2B transcript variant 20	NR_164818.1:n.	N/A	N/A
DENND2B transcript variant 21	NR_164819.1:n.	N/A	N/A
DENND2B transcript variant 22	NR_164820.1:n.	N/A	N/A
DENND2B transcript variant 23	NR_164821.1:n.	N/A	N/A
DENND2B transcript variant 24	NR_164822.1:n.	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	CA=	delCA
GRCh38.p14 chr 11	NC_000011.10:g.8912198_8912199=	NC_000011.10:g.8912198_8912199del
GRCh37.p13 chr 11	NC_000011.9:g.8933745_8933746=	NC_000011.9:g.8933745_8933746del
DENND2B RefSeqGene	NG_029450.1:g.3753_3754=	NG_029450.1:g.3753_3754del
AKIP1 RefSeqGene	NG_030417.1:g.6045_6046=	NG_030417.1:g.6045_6046del
AKIP1 transcript variant 2	NM_001206646.1:c.222+527=	NM_001206646.1:c.222+527_222+528del
AKIP1 transcript variant 2	NM_001206646.2:c.222+527=	NM_001206646.2:c.222+527_222+528del
AKIP1 transcript variant 3	NM_001206647.1:c.223-255=	NM_001206647.1:c.223-255_223-254del
AKIP1 transcript variant 3	NM_001206647.2:c.223-255=	NM_001206647.2:c.223-255_223-254del
AKIP1 transcript variant 4	NM_001206648.1:c.222+527=	NM_001206648.1:c.222+527_222+528del
AKIP1 transcript variant 4	NM_001206648.2:c.222+527=	NM_001206648.2:c.222+527_222+528del
AKIP1 transcript variant 1	NM_020642.3:c.223-255=	NM_020642.3:c.223-255_223-254del
AKIP1 transcript variant 1	NM_020642.4:c.223-255=	NM_020642.4:c.223-255_223-254del
AKIP1 transcript variant X1	XM_017018011.2:c.223-255=	XM_017018011.2:c.223-255_223-254del
AKIP1 transcript variant X2	XM_047427261.1:c.222+527=	XM_047427261.1:c.222+527_222+528del

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#.

3 SubSNP, 3 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss2896158240	Jan 10, 2018 (151)
2	EVA_DECODE	ss3691184851	Jul 13, 2019 (153)
3	TOMMO_GENOMICS	ss5747349577	Oct 16, 2022 (156)
4	gnomAD - Genomes	NC_000011.10 - 8912198	Apr 26, 2021 (155)
5	14KJPN	NC_000011.10 - 8912198	Oct 16, 2022 (156)
6	ALFA	NC_000011.10 - 8912198	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
ss2896158240	NC_000011.9:8933744:CA:	NC_000011.10:8912197:CA:	(self)
370911090, 81186681, 6641374914, ss3691184851, ss5747349577	NC_000011.10:8912197:CA:	NC_000011.10:8912197:CA:	(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 rs1491488457

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

rs1491488457