Name: rs1491586583
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.

rs1491586583

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:184930998-184930999 (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: insC
Variation Type: Insertion
Frequency: insC=0.413546 (42046/101672, GnomAD)
insC=0.31920 (8958/28064, 14KJPN)
insC=0.29827 (4798/16086, 8.3KJPN) (+ 1 more)
insC=0.24591 (2917/11862, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: NIBAN1 : Intron Variant
LOC124904469 : Non Coding Transcript 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	=0.75409	C=0.24591	0.508177	0.491823	32
European	Sub	7618	=0.7066	C=0.2934	0.413232	0.586768	32
African	Sub	2816	=0.8874	C=0.1126	0.774858	0.225142	13
African Others	Sub	108	=0.954	C=0.046	0.907407	0.092593	0
African American	Sub	2708	=0.8848	C=0.1152	0.769572	0.230428	13
Asian	Sub	108	=0.787	C=0.213	0.574074	0.425926	3
East Asian	Sub	84	=0.76	C=0.24	0.52381	0.47619	3
Other Asian	Sub	24	=0.88	C=0.12	0.75	0.25	0
Latin American 1	Sub	146	=0.719	C=0.281	0.438356	0.561644	7
Latin American 2	Sub	610	=0.749	C=0.251	0.498361	0.501639	19
South Asian	Sub	94	=0.65	C=0.35	0.297872	0.702128	8
Other	Sub	470	=0.755	C=0.245	0.510638	0.489362	14

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	101672	- No frequency provided	insC=0.413546
gnomAD - Genomes	European	Sub	63078	- No frequency provided	insC=0.46856
gnomAD - Genomes	African	Sub	20402	- No frequency provided	insC=0.28179
gnomAD - Genomes	American	Sub	10922	- No frequency provided	insC=0.38152
gnomAD - Genomes	Ashkenazi Jewish	Sub	3014	- No frequency provided	insC=0.3716
gnomAD - Genomes	East Asian	Sub	2570	- No frequency provided	insC=0.2926
gnomAD - Genomes	Other	Sub	1686	- No frequency provided	insC=0.4164
14KJPN	JAPANESE	Study-wide	28064	- No frequency provided	insC=0.31920
8.3KJPN	JAPANESE	Study-wide	16086	- No frequency provided	insC=0.29827
Allele Frequency Aggregator	Total	Global	11862	- No frequency provided	insC=0.24591
Allele Frequency Aggregator	European	Sub	7618	- No frequency provided	insC=0.2934
Allele Frequency Aggregator	African	Sub	2816	- No frequency provided	insC=0.1126
Allele Frequency Aggregator	Latin American 2	Sub	610	- No frequency provided	insC=0.251
Allele Frequency Aggregator	Other	Sub	470	- No frequency provided	insC=0.245
Allele Frequency Aggregator	Latin American 1	Sub	146	- No frequency provided	insC=0.281
Allele Frequency Aggregator	Asian	Sub	108	- No frequency provided	insC=0.213
Allele Frequency Aggregator	South Asian	Sub	94	- No frequency provided	insC=0.35

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 1	NC_000001.11:g.184930998_184930999insC
GRCh37.p13 chr 1	NC_000001.10:g.184900130_184900131insC
NIBAN1 RefSeqGene	NG_051588.1:g.48588_48589insG

Gene: NIBAN1, niban apoptosis regulator 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NIBAN1 transcript	NM_052966.4:c.56-31690_56… NM_052966.4:c.56-31690_56-31689insG	N/A	Intron Variant
NIBAN1 transcript variant X1	XM_047444091.1:c.233-3169… XM_047444091.1:c.233-31690_233-31689insG	N/A	Intron Variant
NIBAN1 transcript variant X2	XM_047444093.1:c.233-3169… XM_047444093.1:c.233-31690_233-31689insG	N/A	Intron Variant
NIBAN1 transcript variant X3	XM_047444094.1:c.233-3169… XM_047444094.1:c.233-31690_233-31689insG	N/A	Intron Variant
NIBAN1 transcript variant X4	XM_047444098.1:c.56-31690… XM_047444098.1:c.56-31690_56-31689insG	N/A	Intron Variant
NIBAN1 transcript variant X5	XM_047444102.1:c.56-31690… XM_047444102.1:c.56-31690_56-31689insG	N/A	Intron Variant

Gene: LOC124904469, uncharacterized LOC124904469 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC124904469 transcript variant X1	XR_007066770.1:n.12652_12… XR_007066770.1:n.12652_12653insG	N/A	Non Coding 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	=	insC
GRCh38.p14 chr 1	NC_000001.11:g.184930998_184930999=	NC_000001.11:g.184930998_184930999insC
GRCh37.p13 chr 1	NC_000001.10:g.184900130_184900131=	NC_000001.10:g.184900130_184900131insC
NIBAN1 RefSeqGene	NG_051588.1:g.48588_48589=	NG_051588.1:g.48588_48589insG
LOC124904469 transcript variant X1	XR_007066770.1:n.12652_12653=	XR_007066770.1:n.12652_12653insG
FAM129A transcript	NM_052966.3:c.56-31689=	NM_052966.3:c.56-31689_56-31688insG
NIBAN1 transcript	NM_052966.4:c.56-31690=	NM_052966.4:c.56-31690_56-31689insG
FAM129A transcript variant X1	XM_005244873.1:c.56-31689=	XM_005244873.1:c.56-31689_56-31688insG
NIBAN1 transcript variant X1	XM_047444091.1:c.233-31690=	XM_047444091.1:c.233-31690_233-31689insG
NIBAN1 transcript variant X2	XM_047444093.1:c.233-31690=	XM_047444093.1:c.233-31690_233-31689insG
NIBAN1 transcript variant X3	XM_047444094.1:c.233-31690=	XM_047444094.1:c.233-31690_233-31689insG
NIBAN1 transcript variant X4	XM_047444098.1:c.56-31690=	XM_047444098.1:c.56-31690_56-31689insG
NIBAN1 transcript variant X5	XM_047444102.1:c.56-31690=	XM_047444102.1:c.56-31690_56-31689insG

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#.

11 SubSNP, 4 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SWEGEN	ss2988088113	Jan 10, 2018 (151)
2	PACBIO	ss3794120785	Jul 12, 2019 (153)
3	EVA	ss3826532637	Apr 25, 2020 (154)
4	GNOMAD	ss4007347081	Apr 25, 2021 (155)
5	TOMMO_GENOMICS	ss5147424922	Apr 25, 2021 (155)
6	1000G_HIGH_COVERAGE	ss5245017507	Oct 12, 2022 (156)
7	HUGCELL_USP	ss5445530614	Oct 12, 2022 (156)
8	SANFORD_IMAGENETICS	ss5627003910	Oct 12, 2022 (156)
9	TOMMO_GENOMICS	ss5674895865	Oct 12, 2022 (156)
10	YY_MCH	ss5801440992	Oct 12, 2022 (156)
11	EVA	ss5849191367	Oct 12, 2022 (156)
12	gnomAD - Genomes	NC_000001.11 - 184930999	Apr 25, 2021 (155)
13	8.3KJPN	NC_000001.10 - 184900131	Apr 25, 2021 (155)
14	14KJPN	NC_000001.11 - 184930999	Oct 12, 2022 (156)
15	ALFA	NC_000001.11 - 184930999	Apr 25, 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
5394229, ss2988088113, ss3794120785, ss3826532637, ss5147424922, ss5627003910	NC_000001.10:184900130::C	NC_000001.11:184930998::C	(self)
33083949, 8732969, 14799210071, ss4007347081, ss5245017507, ss5445530614, ss5674895865, ss5801440992, ss5849191367	NC_000001.11:184930998::C	NC_000001.11:184930998::C	(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 rs1491586583

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

rs1491586583