Name: rs1490562186
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.

rs1490562186

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chrX:135344169-135344172 (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: dupAGG
Variation Type: Indel Insertion and Deletion
Frequency: dupAGG=0.000011 (3/264690, TOPMED)
dupAGG=0.00000 (0/14050, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ZNF449 : 2KB Upstream Variant
ZNF75D : 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	HWEP
Total	Global	14050	GAGG=1.00000	GAGGAGG=0.00000	1.0	N/A
European	Sub	9690	GAGG=1.0000	GAGGAGG=0.0000	1.0	N/A
African	Sub	2898	GAGG=1.0000	GAGGAGG=0.0000	1.0	N/A
African Others	Sub	114	GAGG=1.000	GAGGAGG=0.000	1.0	N/A
African American	Sub	2784	GAGG=1.0000	GAGGAGG=0.0000	1.0	N/A
Asian	Sub	112	GAGG=1.000	GAGGAGG=0.000	1.0	N/A
East Asian	Sub	86	GAGG=1.00	GAGGAGG=0.00	1.0	N/A
Other Asian	Sub	26	GAGG=1.00	GAGGAGG=0.00	1.0	N/A
Latin American 1	Sub	146	GAGG=1.000	GAGGAGG=0.000	1.0	N/A
Latin American 2	Sub	610	GAGG=1.000	GAGGAGG=0.000	1.0	N/A
South Asian	Sub	98	GAGG=1.00	GAGGAGG=0.00	1.0	N/A
Other	Sub	496	GAGG=1.000	GAGGAGG=0.000	1.0	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
TopMed	Global	Study-wide	264690	- No frequency provided	dupAGG=0.000011
Allele Frequency Aggregator	Total	Global	14050	GAGG=1.00000	dupAGG=0.00000
Allele Frequency Aggregator	European	Sub	9690	GAGG=1.0000	dupAGG=0.0000
Allele Frequency Aggregator	African	Sub	2898	GAGG=1.0000	dupAGG=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	GAGG=1.000	dupAGG=0.000
Allele Frequency Aggregator	Other	Sub	496	GAGG=1.000	dupAGG=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	GAGG=1.000	dupAGG=0.000
Allele Frequency Aggregator	Asian	Sub	112	GAGG=1.000	dupAGG=0.000
Allele Frequency Aggregator	South Asian	Sub	98	GAGG=1.00	dupAGG=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 X	NC_000023.11:g.135344170_135344172dup
GRCh37.p13 chr X	NC_000023.10:g.134478095_134478097dup
ZNF75D RefSeqGene	NG_021412.2:g.4917_4919dup
ZNF449 RefSeqGene	NG_021220.1:g.4400_4402dup
GRCh37.p13 chr X fix patch HG1443_HG1444_PATCH	NW_004070887.1:g.275313_275315dup

Gene: ZNF75D, zinc finger protein 75D (minus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
ZNF75D transcript variant 1	NM_007131.5:c.	N/A	Upstream Transcript Variant
ZNF75D transcript variant 2	NM_001185063.2:c.	N/A	N/A
ZNF75D transcript variant 3	NR_110381.2:n.	N/A	Upstream Transcript Variant
ZNF75D transcript variant X4	XM_011531397.4:c.	N/A	Upstream Transcript Variant
ZNF75D transcript variant X1	XM_047442485.1:c.	N/A	Upstream Transcript Variant
ZNF75D transcript variant X2	XM_047442486.1:c.	N/A	Upstream Transcript Variant
ZNF75D transcript variant X3	XM_047442487.1:c.	N/A	Upstream Transcript Variant
ZNF75D transcript variant X5	XM_005262471.4:c.	N/A	N/A

Gene: ZNF449, zinc finger protein 449 (plus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
ZNF449 transcript	NM_152695.6:c.	N/A	Upstream Transcript Variant
ZNF449 transcript variant X2	XM_017029351.2:c.	N/A	Upstream Transcript Variant
ZNF449 transcript variant X1	XM_047441914.1:c.	N/A	Upstream Transcript Variant
ZNF449 transcript variant X3	XM_047441915.1:c.	N/A	Upstream 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	GAGG=	dupAGG
GRCh38.p14 chr X	NC_000023.11:g.135344169_135344172=	NC_000023.11:g.135344170_135344172dup
GRCh37.p13 chr X	NC_000023.10:g.134478094_134478097=	NC_000023.10:g.134478095_134478097dup
ZNF75D RefSeqGene	NG_021412.2:g.4916_4919=	NG_021412.2:g.4917_4919dup
ZNF449 RefSeqGene	NG_021220.1:g.4399_4402=	NG_021220.1:g.4400_4402dup
GRCh37.p13 chr X fix patch HG1443_HG1444_PATCH	NW_004070887.1:g.275312_275315=	NW_004070887.1:g.275313_275315dup

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	TOPMED	ss5138280970	Apr 27, 2021 (155)
2	TopMed	NC_000023.11 - 135344169	Apr 27, 2021 (155)
3	ALFA	NC_000023.11 - 135344169	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
701887327, ss5138280970	NC_000023.11:135344168::GAG	NC_000023.11:135344168:GAGG:GAGGAGG	(self)
4450620318	NC_000023.11:135344168:GAGG:GAGGAGG	NC_000023.11:135344168:GAGG:GAGGAGG	(self)

Removed from this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Destination RSIDs
ss2490301017	NC_000023.10:134478093::GAG	NC_000023.11:135344168:GAGG:GAGGAGG

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

No publications for rs1490562186

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

rs1490562186