Name: rs1491551760
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.

rs1491551760

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr16:88181073-88181074 (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: delCT
Variation Type: Deletion
Frequency: delCT=0.000166 (21/126388, GnomAD)
delCT=0.00025 (4/16261, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ZNF469 : Intron Variant
LOC105371401 : 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	16261	CT=0.99975	=0.00025	0.999506	0.000494	0
European	Sub	12010	CT=0.99992	=0.00008	0.999833	0.000167	0
African	Sub	2816	CT=0.9993	=0.0007	0.99858	0.00142	0
African Others	Sub	108	CT=1.000	=0.000	1.0	0.0	N/A
African American	Sub	2708	CT=0.9993	=0.0007	0.998523	0.001477	0
Asian	Sub	108	CT=1.000	=0.000	1.0	0.0	N/A
East Asian	Sub	84	CT=1.00	=0.00	1.0	0.0	N/A
Other Asian	Sub	24	CT=1.00	=0.00	1.0	0.0	N/A
Latin American 1	Sub	146	CT=1.000	=0.000	1.0	0.0	N/A
Latin American 2	Sub	610	CT=0.998	=0.002	0.996721	0.003279	0
South Asian	Sub	94	CT=1.00	=0.00	1.0	0.0	N/A
Other	Sub	477	CT=1.000	=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	126388	CT=0.999834	delCT=0.000166
gnomAD - Genomes	European	Sub	70978	CT=0.99997	delCT=0.00003
gnomAD - Genomes	African	Sub	35318	CT=0.99952	delCT=0.00048
gnomAD - Genomes	American	Sub	12286	CT=0.99984	delCT=0.00016
gnomAD - Genomes	Ashkenazi Jewish	Sub	3162	CT=1.0000	delCT=0.0000
gnomAD - Genomes	East Asian	Sub	2720	CT=1.0000	delCT=0.0000
gnomAD - Genomes	Other	Sub	1924	CT=1.0000	delCT=0.0000
Allele Frequency Aggregator	Total	Global	16261	CT=0.99975	delCT=0.00025
Allele Frequency Aggregator	European	Sub	12010	CT=0.99992	delCT=0.00008
Allele Frequency Aggregator	African	Sub	2816	CT=0.9993	delCT=0.0007
Allele Frequency Aggregator	Latin American 2	Sub	610	CT=0.998	delCT=0.002
Allele Frequency Aggregator	Other	Sub	477	CT=1.000	delCT=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	CT=1.000	delCT=0.000
Allele Frequency Aggregator	Asian	Sub	108	CT=1.000	delCT=0.000
Allele Frequency Aggregator	South Asian	Sub	94	CT=1.00	delCT=0.00

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 16	NC_000016.10:g.88181073_88181074del
GRCh37.p13 chr 16	NC_000016.9:g.88214679_88214680del

Gene: ZNF469, zinc finger protein 469 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ZNF469 transcript	NM_001367624.2:c.	N/A	Genic Upstream Transcript Variant
ZNF469 transcript variant X1	XM_047434810.1:c.-294+800… XM_047434810.1:c.-294+80004_-294+80005del	N/A	Intron Variant

Gene: LOC105371401, uncharacterized LOC105371401 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105371401 transcript variant X1	XR_007065176.1:n.5570_557… XR_007065176.1:n.5570_5571del	N/A	Non Coding Transcript Variant
LOC105371401 transcript variant X2	XR_007065177.1: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	CT=	delCT
GRCh38.p14 chr 16	NC_000016.10:g.88181073_88181074=	NC_000016.10:g.88181073_88181074del
GRCh37.p13 chr 16	NC_000016.9:g.88214679_88214680=	NC_000016.9:g.88214679_88214680del
LOC105371401 transcript variant X1	XR_007065176.1:n.5570_5571=	XR_007065176.1:n.5570_5571del
ZNF469 transcript variant X1	XM_047434810.1:c.-294+80004=	XM_047434810.1:c.-294+80004_-294+80005del

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#.

1 SubSNP, 2 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss4306193666	Apr 27, 2021 (155)
2	gnomAD - Genomes	NC_000016.10 - 88181073	Apr 27, 2021 (155)
3	ALFA	NC_000016.10 - 88181073	Apr 27, 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
498460290, 3604333076, ss4306193666	NC_000016.10:88181072:CT:	NC_000016.10:88181072:CT:	(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 rs1491551760

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

rs1491551760