Name: rs73233339
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.

rs73233339

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr21:42920423 (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: A>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.027534 (7288/264690, TOPMED)
C=0.026179 (3669/140150, GnomAD)
C=0.05096 (1440/28258, 14KJPN) (+ 18 more)
C=0.02837 (536/18890, ALFA)
C=0.05101 (855/16760, 8.3KJPN)
C=0.0386 (247/6404, 1000G_30x)
C=0.0397 (199/5008, 1000G)
C=0.0203 (91/4480, Estonian)
C=0.0270 (104/3854, ALSPAC)
C=0.0272 (101/3708, TWINSUK)
C=0.0522 (153/2930, KOREAN)
C=0.0519 (95/1832, Korea1K)
C=0.026 (26/998, GoNL)
C=0.013 (8/600, NorthernSweden)
C=0.111 (24/216, Qatari)
C=0.047 (10/214, Vietnamese)
A=0.50 (26/52, SGDP_PRJ)
C=0.50 (26/52, SGDP_PRJ)
C=0.03 (1/40, GENOME_DK)
A=0.5 (2/4, Siberian)
C=0.5 (2/4, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ERVH48-1 : 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	18890	A=0.97163	C=0.02837
European	Sub	14286	A=0.96997	C=0.03003
African	Sub	2946	A=0.9817	C=0.0183
African Others	Sub	114	A=0.982	C=0.018
African American	Sub	2832	A=0.9816	C=0.0184
Asian	Sub	112	A=0.964	C=0.036
East Asian	Sub	86	A=0.95	C=0.05
Other Asian	Sub	26	A=1.00	C=0.00
Latin American 1	Sub	146	A=0.952	C=0.048
Latin American 2	Sub	610	A=0.980	C=0.020
South Asian	Sub	98	A=0.90	C=0.10
Other	Sub	692	A=0.971	C=0.029

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	A=0.972466	C=0.027534
gnomAD - Genomes	Global	Study-wide	140150	A=0.973821	C=0.026179
gnomAD - Genomes	European	Sub	75912	A=0.97147	C=0.02853
gnomAD - Genomes	African	Sub	41992	A=0.98378	C=0.01622
gnomAD - Genomes	American	Sub	13642	A=0.96789	C=0.03211
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=0.9576	C=0.0424
gnomAD - Genomes	East Asian	Sub	3128	A=0.9421	C=0.0579
gnomAD - Genomes	Other	Sub	2152	A=0.9712	C=0.0288
14KJPN	JAPANESE	Study-wide	28258	A=0.94904	C=0.05096
Allele Frequency Aggregator	Total	Global	18890	A=0.97163	C=0.02837
Allele Frequency Aggregator	European	Sub	14286	A=0.96997	C=0.03003
Allele Frequency Aggregator	African	Sub	2946	A=0.9817	C=0.0183
Allele Frequency Aggregator	Other	Sub	692	A=0.971	C=0.029
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.980	C=0.020
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.952	C=0.048
Allele Frequency Aggregator	Asian	Sub	112	A=0.964	C=0.036
Allele Frequency Aggregator	South Asian	Sub	98	A=0.90	C=0.10
8.3KJPN	JAPANESE	Study-wide	16760	A=0.94899	C=0.05101
1000Genomes_30x	Global	Study-wide	6404	A=0.9614	C=0.0386
1000Genomes_30x	African	Sub	1786	A=0.9854	C=0.0146
1000Genomes_30x	Europe	Sub	1266	A=0.9724	C=0.0276
1000Genomes_30x	South Asian	Sub	1202	A=0.8960	C=0.1040
1000Genomes_30x	East Asian	Sub	1170	A=0.9615	C=0.0385
1000Genomes_30x	American	Sub	980	A=0.984	C=0.016
1000Genomes	Global	Study-wide	5008	A=0.9603	C=0.0397
1000Genomes	African	Sub	1322	A=0.9849	C=0.0151
1000Genomes	East Asian	Sub	1008	A=0.9633	C=0.0367
1000Genomes	Europe	Sub	1006	A=0.9732	C=0.0268
1000Genomes	South Asian	Sub	978	A=0.896	C=0.104
1000Genomes	American	Sub	694	A=0.981	C=0.019
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.9797	C=0.0203
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.9730	C=0.0270
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.9728	C=0.0272
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.9478	C=0.0522
Korean Genome Project	KOREAN	Study-wide	1832	A=0.9481	C=0.0519
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.974	C=0.026
Northern Sweden	ACPOP	Study-wide	600	A=0.987	C=0.013
Qatari	Global	Study-wide	216	A=0.889	C=0.111
A Vietnamese Genetic Variation Database	Global	Study-wide	214	A=0.953	C=0.047
SGDP_PRJ	Global	Study-wide	52	A=0.50	C=0.50
The Danish reference pan genome	Danish	Study-wide	40	A=0.97	C=0.03
Siberian	Global	Study-wide	4	A=0.5	C=0.5

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 21	NC_000021.9:g.42920423A>C
GRCh37.p13 chr 21	NC_000021.8:g.44340533A>C

Gene: ERVH48-1, endogenous retrovirus group 48 member 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ERVH48-1 transcript	NM_001308491.2:c.-285-113… NM_001308491.2:c.-285-1132T>G	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	A=	C
GRCh38.p14 chr 21	NC_000021.9:g.42920423=	NC_000021.9:g.42920423A>C
GRCh37.p13 chr 21	NC_000021.8:g.44340533=	NC_000021.8:g.44340533A>C
ERVH48-1 transcript	NM_001308491.2:c.-285-1132=	NM_001308491.2:c.-285-1132T>G
LOC100996619 transcript	XM_003846299.3:c.512-1132=	XM_003846299.3:c.512-1132T>G

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#.

45 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss112510233	Feb 14, 2009 (130)
2	1000GENOMES	ss228589032	Jul 14, 2010 (132)
3	1000GENOMES	ss238000402	Jul 15, 2010 (132)
4	GMI	ss283558163	May 04, 2012 (137)
5	SSMP	ss662436177	Apr 25, 2013 (138)
6	EVA-GONL	ss995163142	Aug 21, 2014 (142)
7	1000GENOMES	ss1366451472	Aug 21, 2014 (142)
8	DDI	ss1429198254	Apr 01, 2015 (144)
9	EVA_GENOME_DK	ss1579681226	Apr 01, 2015 (144)
10	EVA_UK10K_ALSPAC	ss1639650313	Apr 01, 2015 (144)
11	EVA_UK10K_TWINSUK	ss1682644346	Apr 01, 2015 (144)
12	EVA_DECODE	ss1699234688	Apr 01, 2015 (144)
13	WEILL_CORNELL_DGM	ss1938713799	Feb 12, 2016 (147)
14	JJLAB	ss2030131735	Sep 14, 2016 (149)
15	USC_VALOUEV	ss2158736806	Dec 20, 2016 (150)
16	HUMAN_LONGEVITY	ss2246108765	Dec 20, 2016 (150)
17	SYSTEMSBIOZJU	ss2629564794	Nov 08, 2017 (151)
18	GRF	ss2704467781	Nov 08, 2017 (151)
19	GNOMAD	ss2972240795	Nov 08, 2017 (151)
20	SWEGEN	ss3018960023	Nov 08, 2017 (151)
21	CSHL	ss3352740313	Nov 08, 2017 (151)
22	EGCUT_WGS	ss3685537069	Jul 13, 2019 (153)
23	EVA_DECODE	ss3707817459	Jul 13, 2019 (153)
24	ACPOP	ss3743770472	Jul 13, 2019 (153)
25	EVA	ss3759160498	Jul 13, 2019 (153)
26	KHV_HUMAN_GENOMES	ss3822326490	Jul 13, 2019 (153)
27	EVA	ss3841576758	Apr 27, 2020 (154)
28	EVA	ss3847090475	Apr 27, 2020 (154)
29	SGDP_PRJ	ss3890093620	Apr 27, 2020 (154)
30	KRGDB	ss3940439426	Apr 27, 2020 (154)
31	KOGIC	ss3983175714	Apr 27, 2020 (154)
32	TOPMED	ss5102983506	Apr 27, 2021 (155)
33	TOMMO_GENOMICS	ss5231713746	Apr 27, 2021 (155)
34	1000G_HIGH_COVERAGE	ss5310362619	Oct 16, 2022 (156)
35	EVA	ss5440153527	Oct 16, 2022 (156)
36	HUGCELL_USP	ss5502397306	Oct 16, 2022 (156)
37	EVA	ss5512335358	Oct 16, 2022 (156)
38	1000G_HIGH_COVERAGE	ss5617570765	Oct 16, 2022 (156)
39	SANFORD_IMAGENETICS	ss5664098545	Oct 16, 2022 (156)
40	TOMMO_GENOMICS	ss5792279601	Oct 16, 2022 (156)
41	YY_MCH	ss5818480717	Oct 16, 2022 (156)
42	EVA	ss5839100203	Oct 16, 2022 (156)
43	EVA	ss5853324386	Oct 16, 2022 (156)
44	EVA	ss5892524981	Oct 16, 2022 (156)
45	EVA	ss5958997912	Oct 16, 2022 (156)
46	1000Genomes	NC_000021.8 - 44340533	Oct 12, 2018 (152)
47	1000Genomes_30x	NC_000021.9 - 42920423	Oct 16, 2022 (156)
48	The Avon Longitudinal Study of Parents and Children	NC_000021.8 - 44340533	Oct 12, 2018 (152)
49	Genetic variation in the Estonian population	NC_000021.8 - 44340533	Oct 12, 2018 (152)
50	The Danish reference pan genome	NC_000021.8 - 44340533	Apr 27, 2020 (154)
51	gnomAD - Genomes	NC_000021.9 - 42920423	Apr 27, 2021 (155)
52	Genome of the Netherlands Release 5	NC_000021.8 - 44340533	Apr 27, 2020 (154)
53	KOREAN population from KRGDB	NC_000021.8 - 44340533	Apr 27, 2020 (154)
54	Korean Genome Project	NC_000021.9 - 42920423	Apr 27, 2020 (154)
55	Northern Sweden	NC_000021.8 - 44340533	Jul 13, 2019 (153)
56	Qatari	NC_000021.8 - 44340533	Apr 27, 2020 (154)
57	SGDP_PRJ	NC_000021.8 - 44340533	Apr 27, 2020 (154)
58	Siberian	NC_000021.8 - 44340533	Apr 27, 2020 (154)
59	8.3KJPN	NC_000021.8 - 44340533	Apr 27, 2021 (155)
60	14KJPN	NC_000021.9 - 42920423	Oct 16, 2022 (156)
61	TopMed	NC_000021.9 - 42920423	Apr 27, 2021 (155)
62	UK 10K study - Twins	NC_000021.8 - 44340533	Oct 12, 2018 (152)
63	A Vietnamese Genetic Variation Database	NC_000021.8 - 44340533	Jul 13, 2019 (153)
64	ALFA	NC_000021.9 - 42920423	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
ss112510233, ss283558163, ss1699234688	NC_000021.7:43213601:A:C	NC_000021.9:42920422:A:C	(self)
79977590, 44267163, 31275317, 5846165, 19719679, 47616820, 17055337, 20755721, 42110600, 11253160, 89683053, 44267163, 9767641, ss228589032, ss238000402, ss662436177, ss995163142, ss1366451472, ss1429198254, ss1579681226, ss1639650313, ss1682644346, ss1938713799, ss2030131735, ss2158736806, ss2629564794, ss2704467781, ss2972240795, ss3018960023, ss3352740313, ss3685537069, ss3743770472, ss3759160498, ss3841576758, ss3890093620, ss3940439426, ss5231713746, ss5440153527, ss5512335358, ss5664098545, ss5839100203, ss5958997912	NC_000021.8:44340532:A:C	NC_000021.9:42920422:A:C	(self)
105096700, 564313589, 39553715, 126116705, 378092452, 5290709674, ss2246108765, ss3707817459, ss3822326490, ss3847090475, ss3983175714, ss5102983506, ss5310362619, ss5502397306, ss5617570765, ss5792279601, ss5818480717, ss5853324386, ss5892524981	NC_000021.9:42920422:A:C	NC_000021.9:42920422:A: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 rs73233339

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

rs73233339