Name: rs148841346
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.

rs148841346

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr10:45000415 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.000159 (42/264690, TOPMED)
T=0.000954 (232/243300, GnomAD_exome)
T=0.000368 (71/193086, ALFA) (+ 9 more)
T=0.000135 (19/140270, GnomAD)
T=0.00128 (121/94420, ExAC)
T=0.00015 (2/13006, GO-ESP)
T=0.0009 (6/6404, 1000G_30x)
T=0.0012 (6/5008, 1000G)
T=0.0002 (1/4480, Estonian)
T=0.0003 (1/3854, ALSPAC)
T=0.0000 (0/3708, TWINSUK)
T=0.005 (1/216, Qatari)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ZNF22-AS1 : Non Coding Transcript Variant
ZNF22 : 2KB Upstream 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	193208	G=0.999633	T=0.000367
European	Sub	168292	G=0.999703	T=0.000297
African	Sub	4960	G=0.9998	T=0.0002
African Others	Sub	176	G=1.000	T=0.000
African American	Sub	4784	G=0.9998	T=0.0002
Asian	Sub	3360	G=1.0000	T=0.0000
East Asian	Sub	2678	G=1.0000	T=0.0000
Other Asian	Sub	682	G=1.000	T=0.000
Latin American 1	Sub	796	G=1.000	T=0.000
Latin American 2	Sub	968	G=1.000	T=0.000
South Asian	Sub	274	G=0.996	T=0.004
Other	Sub	14558	G=0.99869	T=0.00131

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	G=0.999841	T=0.000159
gnomAD - Exomes	Global	Study-wide	243300	G=0.999046	T=0.000954
gnomAD - Exomes	European	Sub	129946	G=0.999823	T=0.000177
gnomAD - Exomes	Asian	Sub	47718	G=0.99623	T=0.00377
gnomAD - Exomes	American	Sub	34100	G=0.99988	T=0.00012
gnomAD - Exomes	African	Sub	15618	G=1.00000	T=0.00000
gnomAD - Exomes	Ashkenazi Jewish	Sub	9926	G=0.9982	T=0.0018
gnomAD - Exomes	Other	Sub	5992	G=0.9988	T=0.0012
Allele Frequency Aggregator	Total	Global	193086	G=0.999632	T=0.000368
Allele Frequency Aggregator	European	Sub	168188	G=0.999703	T=0.000297
Allele Frequency Aggregator	Other	Sub	14554	G=0.99869	T=0.00131
Allele Frequency Aggregator	African	Sub	4946	G=0.9998	T=0.0002
Allele Frequency Aggregator	Asian	Sub	3360	G=1.0000	T=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	968	G=1.000	T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	796	G=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	274	G=0.996	T=0.004
gnomAD - Genomes	Global	Study-wide	140270	G=0.999865	T=0.000135
gnomAD - Genomes	European	Sub	75948	G=0.99987	T=0.00013
gnomAD - Genomes	African	Sub	42046	G=1.00000	T=0.00000
gnomAD - Genomes	American	Sub	13664	G=0.99978	T=0.00022
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=0.9982	T=0.0018
gnomAD - Genomes	East Asian	Sub	3134	G=1.0000	T=0.0000
gnomAD - Genomes	Other	Sub	2154	G=1.0000	T=0.0000
ExAC	Global	Study-wide	94420	G=0.99872	T=0.00128
ExAC	Europe	Sub	57442	G=0.99956	T=0.00044
ExAC	Asian	Sub	19786	G=0.99525	T=0.00475
ExAC	American	Sub	8512	G=1.0000	T=0.0000
ExAC	African	Sub	8024	G=1.0000	T=0.0000
ExAC	Other	Sub	656	G=0.997	T=0.003
GO Exome Sequencing Project	Global	Study-wide	13006	G=0.99985	T=0.00015
GO Exome Sequencing Project	European American	Sub	8600	G=0.9998	T=0.0002
GO Exome Sequencing Project	African American	Sub	4406	G=1.0000	T=0.0000
1000Genomes_30x	Global	Study-wide	6404	G=0.9991	T=0.0009
1000Genomes_30x	African	Sub	1786	G=1.0000	T=0.0000
1000Genomes_30x	Europe	Sub	1266	G=0.9992	T=0.0008
1000Genomes_30x	South Asian	Sub	1202	G=0.9958	T=0.0042
1000Genomes_30x	East Asian	Sub	1170	G=1.0000	T=0.0000
1000Genomes_30x	American	Sub	980	G=1.000	T=0.000
1000Genomes	Global	Study-wide	5008	G=0.9988	T=0.0012
1000Genomes	African	Sub	1322	G=1.0000	T=0.0000
1000Genomes	East Asian	Sub	1008	G=1.0000	T=0.0000
1000Genomes	Europe	Sub	1006	G=0.9990	T=0.0010
1000Genomes	South Asian	Sub	978	G=0.995	T=0.005
1000Genomes	American	Sub	694	G=1.000	T=0.000
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.9998	T=0.0002
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9997	T=0.0003
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=1.0000	T=0.0000
Qatari	Global	Study-wide	216	G=0.995	T=0.005

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.45000415G>T
GRCh37.p13 chr 10	NC_000010.10:g.45495863G>T

Gene: ZNF22, zinc finger protein 22 (plus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
ZNF22 transcript	NM_006963.5:c.	N/A	Upstream Transcript Variant

Gene: ZNF22-AS1, ZNF22 antisense RNA 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ZNF22-AS1 transcript variant 2	NR_126421.2:n.276C>A	N/A	Non Coding Transcript Variant
ZNF22-AS1 transcript variant 1	NR_164113.1:n.276C>A	N/A	Non Coding Transcript Variant

Gene: LOC124902530, uncharacterized LOC124902530 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC124902530 transcript	XM_047426129.1:c.274-365G… XM_047426129.1:c.274-365G>T	N/A	Intron 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	G=	T
GRCh38.p14 chr 10	NC_000010.11:g.45000415=	NC_000010.11:g.45000415G>T
GRCh37.p13 chr 10	NC_000010.10:g.45495863=	NC_000010.10:g.45495863G>T
C10orf25 transcript variant 1	NM_001039380.3:c.332=	NM_001039380.3:c.332C>A
C10orf25 transcript	NM_001039380.2:c.332=	NM_001039380.2:c.332C>A
ZNF22-AS1 transcript variant 2	NR_126421.2:n.276=	NR_126421.2:n.276C>A
C10orf25 transcript variant 2	NR_126421.1:n.383=	NR_126421.1:n.383C>A
ZNF22-AS1 transcript variant 1	NR_164113.1:n.276=	NR_164113.1:n.276C>A
C10orf25 transcript	NM_145022.1:c.332=	NM_145022.1:c.332C>A
uncharacterized protein C10orf25 precursor	NP_001034469.2:p.Ala111=	NP_001034469.2:p.Ala111Asp
LOC124902530 transcript	XM_047426129.1:c.274-365=	XM_047426129.1:c.274-365G>T

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#.

42 SubSNP, 12 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	NHLBI-ESP	ss342296753	May 09, 2011 (134)
2	1000GENOMES	ss488930022	May 04, 2012 (137)
3	EXOME_CHIP	ss491434585	May 04, 2012 (137)
4	ILLUMINA	ss780885869	Sep 08, 2015 (146)
5	ILLUMINA	ss783571953	Sep 08, 2015 (146)
6	1000GENOMES	ss1337246106	Aug 21, 2014 (142)
7	EVA_UK10K_ALSPAC	ss1624478776	Apr 01, 2015 (144)
8	EVA_UK10K_TWINSUK	ss1667472809	Apr 01, 2015 (144)
9	EVA_EXAC	ss1689883605	Apr 01, 2015 (144)
10	ILLUMINA	ss1751969156	Sep 08, 2015 (146)
11	ILLUMINA	ss1917846385	Feb 12, 2016 (147)
12	WEILL_CORNELL_DGM	ss1930789729	Feb 12, 2016 (147)
13	ILLUMINA	ss1946281181	Feb 12, 2016 (147)
14	HUMAN_LONGEVITY	ss2174431676	Dec 20, 2016 (150)
15	GNOMAD	ss2738216091	Nov 08, 2017 (151)
16	GNOMAD	ss2748378343	Nov 08, 2017 (151)
17	GNOMAD	ss2888198307	Nov 08, 2017 (151)
18	ILLUMINA	ss3021235454	Nov 08, 2017 (151)
19	ILLUMINA	ss3626437024	Oct 12, 2018 (152)
20	ILLUMINA	ss3634401237	Oct 12, 2018 (152)
21	ILLUMINA	ss3640108579	Oct 12, 2018 (152)
22	ILLUMINA	ss3644533870	Oct 12, 2018 (152)
23	ILLUMINA	ss3651587368	Oct 12, 2018 (152)
24	EGCUT_WGS	ss3673824578	Jul 13, 2019 (153)
25	EVA_DECODE	ss3689784669	Jul 13, 2019 (153)
26	ILLUMINA	ss3725153916	Jul 13, 2019 (153)
27	ILLUMINA	ss3744366247	Jul 13, 2019 (153)
28	ILLUMINA	ss3744702140	Jul 13, 2019 (153)
29	ILLUMINA	ss3772202727	Jul 13, 2019 (153)
30	EVA	ss3824514649	Apr 26, 2020 (154)
31	EVA	ss3825774667	Apr 26, 2020 (154)
32	EVA	ss3986482346	Apr 26, 2021 (155)
33	TOPMED	ss4850717806	Apr 26, 2021 (155)
34	1000G_HIGH_COVERAGE	ss5283847619	Oct 16, 2022 (156)
35	EVA	ss5393131865	Oct 16, 2022 (156)
36	HUGCELL_USP	ss5479482960	Oct 16, 2022 (156)
37	1000G_HIGH_COVERAGE	ss5577685843	Oct 16, 2022 (156)
38	SANFORD_IMAGENETICS	ss5649177877	Oct 16, 2022 (156)
39	EVA	ss5847594092	Oct 16, 2022 (156)
40	EVA	ss5878720648	Oct 16, 2022 (156)
41	EVA	ss5940457939	Oct 16, 2022 (156)
42	EVA	ss5979324231	Oct 16, 2022 (156)
43	1000Genomes	NC_000010.10 - 45495863	Oct 12, 2018 (152)
44	1000Genomes_30x	NC_000010.11 - 45000415	Oct 16, 2022 (156)
45	The Avon Longitudinal Study of Parents and Children	NC_000010.10 - 45495863	Oct 12, 2018 (152)
46	Genetic variation in the Estonian population	NC_000010.10 - 45495863	Oct 12, 2018 (152)
47	ExAC	NC_000010.10 - 45495863	Oct 12, 2018 (152)
48	gnomAD - Genomes	NC_000010.11 - 45000415	Apr 26, 2021 (155)
49	gnomAD - Exomes	NC_000010.10 - 45495863	Jul 13, 2019 (153)
50	GO Exome Sequencing Project	NC_000010.10 - 45495863	Oct 12, 2018 (152)
51	Qatari	NC_000010.10 - 45495863	Apr 26, 2020 (154)
52	TopMed	NC_000010.11 - 45000415	Apr 26, 2021 (155)
53	UK 10K study - Twins	NC_000010.10 - 45495863	Oct 12, 2018 (152)
54	ALFA	NC_000010.11 - 45000415	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
49626533, 27556955, 19562826, 103339, 7414195, 972364, 12831659, 27556955, ss342296753, ss488930022, ss491434585, ss780885869, ss783571953, ss1337246106, ss1624478776, ss1667472809, ss1689883605, ss1751969156, ss1917846385, ss1930789729, ss1946281181, ss2738216091, ss2748378343, ss2888198307, ss3021235454, ss3626437024, ss3634401237, ss3640108579, ss3644533870, ss3651587368, ss3673824578, ss3744366247, ss3744702140, ss3772202727, ss3824514649, ss3825774667, ss3986482346, ss5393131865, ss5649177877, ss5847594092, ss5940457939, ss5979324231	NC_000010.10:45495862:G:T	NC_000010.11:45000414:G:T	(self)
65211778, 350705387, 66263461, 9063398276, ss2174431676, ss3689784669, ss3725153916, ss4850717806, ss5283847619, ss5479482960, ss5577685843, ss5878720648	NC_000010.11:45000414:G:T	NC_000010.11:45000414:G:T	(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 rs148841346

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

rs148841346