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dbSNP Short Genetic Variations

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.

rs75005490

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr10:44998425 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.017265 (4570/264690, TOPMED)
A=0.016665 (2337/140230, GnomAD)
A=0.00637 (164/25750, ALFA) (+ 5 more)
A=0.0186 (119/6404, 1000G_30x)
A=0.0176 (88/5008, 1000G)
A=0.014 (3/216, Qatari)
G=0.5 (4/8, SGDP_PRJ)
A=0.5 (4/8, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ZNF22-AS1 : Non Coding Transcript Variant
LOC124902530 : 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 25750 G=0.99363 A=0.00637
European Sub 20274 G=0.99961 A=0.00039
African Sub 3168 G=0.9545 A=0.0455
African Others Sub 124 G=0.935 A=0.065
African American Sub 3044 G=0.9553 A=0.0447
Asian Sub 128 G=1.000 A=0.000
East Asian Sub 100 G=1.00 A=0.00
Other Asian Sub 28 G=1.00 A=0.00
Latin American 1 Sub 168 G=0.988 A=0.012
Latin American 2 Sub 700 G=0.999 A=0.001
South Asian Sub 114 G=1.000 A=0.000
Other Sub 1198 G=0.9925 A=0.0075


Help

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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 G=0.982735 A=0.017265
gnomAD - Genomes Global Study-wide 140230 G=0.983335 A=0.016665
gnomAD - Genomes European Sub 75956 G=0.99980 A=0.00020
gnomAD - Genomes African Sub 42012 G=0.94778 A=0.05222
gnomAD - Genomes American Sub 13658 G=0.99275 A=0.00725
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3132 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2152 G=0.9865 A=0.0135
Allele Frequency Aggregator Total Global 25750 G=0.99363 A=0.00637
Allele Frequency Aggregator European Sub 20274 G=0.99961 A=0.00039
Allele Frequency Aggregator African Sub 3168 G=0.9545 A=0.0455
Allele Frequency Aggregator Other Sub 1198 G=0.9925 A=0.0075
Allele Frequency Aggregator Latin American 2 Sub 700 G=0.999 A=0.001
Allele Frequency Aggregator Latin American 1 Sub 168 G=0.988 A=0.012
Allele Frequency Aggregator Asian Sub 128 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 114 G=1.000 A=0.000
1000Genomes_30x Global Study-wide 6404 G=0.9814 A=0.0186
1000Genomes_30x African Sub 1786 G=0.9395 A=0.0605
1000Genomes_30x Europe Sub 1266 G=1.0000 A=0.0000
1000Genomes_30x South Asian Sub 1202 G=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000
1000Genomes_30x American Sub 980 G=0.989 A=0.011
1000Genomes Global Study-wide 5008 G=0.9824 A=0.0176
1000Genomes African Sub 1322 G=0.9395 A=0.0605
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=0.988 A=0.012
Qatari Global Study-wide 216 G=0.986 A=0.014
SGDP_PRJ Global Study-wide 8 G=0.5 A=0.5
Help

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 10 NC_000010.11:g.44998425G>A
GRCh37.p13 chr 10 NC_000010.10:g.45493873G>A
Gene: ZNF22-AS1, ZNF22 antisense RNA 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ZNF22-AS1 transcript variant 1 NR_164113.1:n.2266C>T N/A Non Coding Transcript Variant
ZNF22-AS1 transcript variant 2 NR_126421.2:n. N/A Intron Variant
Gene: LOC124902530, uncharacterized LOC124902530 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC124902530 transcript XM_047426129.1:c.274-2355…

XM_047426129.1:c.274-2355G>A

N/A Intron Variant
Help

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
Help

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 G= A
GRCh38.p14 chr 10 NC_000010.11:g.44998425= NC_000010.11:g.44998425G>A
GRCh37.p13 chr 10 NC_000010.10:g.45493873= NC_000010.10:g.45493873G>A
C10orf25 transcript variant 1 NM_001039380.3:c.*1953= NM_001039380.3:c.*1953C>T
C10orf25 transcript NM_001039380.2:c.*1953= NM_001039380.2:c.*1953C>T
ZNF22-AS1 transcript variant 1 NR_164113.1:n.2266= NR_164113.1:n.2266C>T
C10orf25 transcript NM_145022.1:c.*1953= NM_145022.1:c.*1953C>T
LOC124902530 transcript XM_047426129.1:c.274-2355= XM_047426129.1:c.274-2355G>A
Help

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#.

25 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss224697156 Jul 14, 2010 (132)
2 ILLUMINA ss482409622 May 04, 2012 (137)
3 ILLUMINA ss482594697 May 04, 2012 (137)
4 ILLUMINA ss534636858 Sep 08, 2015 (146)
5 TISHKOFF ss561924417 Apr 25, 2013 (138)
6 ILLUMINA ss779365723 Sep 08, 2015 (146)
7 ILLUMINA ss781751975 Sep 08, 2015 (146)
8 ILLUMINA ss834833993 Sep 08, 2015 (146)
9 1000GENOMES ss1337246056 Aug 21, 2014 (142)
10 WEILL_CORNELL_DGM ss1930789719 Feb 12, 2016 (147)
11 HUMAN_LONGEVITY ss2174431574 Dec 20, 2016 (150)
12 ILLUMINA ss2632705423 Nov 08, 2017 (151)
13 GNOMAD ss2888198159 Nov 08, 2017 (151)
14 ILLUMINA ss3626437016 Oct 12, 2018 (152)
15 ILLUMINA ss3630731581 Oct 12, 2018 (152)
16 KHV_HUMAN_GENOMES ss3813416973 Jul 13, 2019 (153)
17 SGDP_PRJ ss3874070271 Apr 26, 2020 (154)
18 TOPMED ss4850717343 Apr 26, 2021 (155)
19 1000G_HIGH_COVERAGE ss5283847583 Oct 16, 2022 (156)
20 EVA ss5393131780 Oct 16, 2022 (156)
21 HUGCELL_USP ss5479482926 Oct 16, 2022 (156)
22 1000G_HIGH_COVERAGE ss5577685779 Oct 16, 2022 (156)
23 SANFORD_IMAGENETICS ss5649177859 Oct 16, 2022 (156)
24 EVA ss5878720596 Oct 16, 2022 (156)
25 EVA ss5940457917 Oct 16, 2022 (156)
26 1000Genomes NC_000010.10 - 45493873 Oct 12, 2018 (152)
27 1000Genomes_30x NC_000010.11 - 44998425 Oct 16, 2022 (156)
28 gnomAD - Genomes NC_000010.11 - 44998425 Apr 26, 2021 (155)
29 Qatari NC_000010.10 - 45493873 Apr 26, 2020 (154)
30 SGDP_PRJ NC_000010.10 - 45493873 Apr 26, 2020 (154)
31 TopMed NC_000010.11 - 44998425 Apr 26, 2021 (155)
32 ALFA NC_000010.11 - 44998425 Apr 26, 2021 (155)
Help

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
ss482594697 NC_000010.9:44813878:G:A NC_000010.11:44998424:G:A (self)
49626480, 12831649, 26087251, ss224697156, ss482409622, ss534636858, ss561924417, ss779365723, ss781751975, ss834833993, ss1337246056, ss1930789719, ss2632705423, ss2888198159, ss3626437016, ss3630731581, ss3874070271, ss5393131780, ss5649177859, ss5940457917 NC_000010.10:45493872:G:A NC_000010.11:44998424:G:A (self)
65211714, 350705025, 66262998, 5172856945, ss2174431574, ss3813416973, ss4850717343, ss5283847583, ss5479482926, ss5577685779, ss5878720596 NC_000010.11:44998424:G:A NC_000010.11:44998424:G:A (self)
Help

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

No publications for rs75005490

Help

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.

Software version is: 2.0.1.post761+d5e8e07