Name: rs79027258
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.

rs79027258

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr19:4060775 (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=0.027164 (7190/264690, TOPMED)
A=0.030696 (4302/140150, GnomAD)
A=0.03489 (659/18890, ALFA) (+ 12 more)
A=0.0131 (84/6404, 1000G_30x)
A=0.0128 (64/5008, 1000G)
A=0.0333 (149/4480, Estonian)
A=0.0011 (2/1832, Korea1K)
A=0.034 (34/998, GoNL)
A=0.032 (19/600, NorthernSweden)
A=0.014 (3/216, Qatari)
A=0.12 (5/40, GENOME_DK)
G=0.5 (4/8, SGDP_PRJ)
A=0.5 (4/8, SGDP_PRJ)
G=0.5 (1/2, Siberian)
A=0.5 (1/2, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ZBTB7A : 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	G=0.96511	A=0.03489
European	Sub	14286	G=0.95786	A=0.04214
African	Sub	2946	G=0.9919	A=0.0081
African Others	Sub	114	G=0.991	A=0.009
African American	Sub	2832	G=0.9919	A=0.0081
Asian	Sub	112	G=1.000	A=0.000
East Asian	Sub	86	G=1.00	A=0.00
Other Asian	Sub	26	G=1.00	A=0.00
Latin American 1	Sub	146	G=0.973	A=0.027
Latin American 2	Sub	610	G=0.974	A=0.026
South Asian	Sub	98	G=1.00	A=0.00
Other	Sub	692	G=0.981	A=0.019

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=0.972836	A=0.027164
gnomAD - Genomes	Global	Study-wide	140150	G=0.969304	A=0.030696
gnomAD - Genomes	European	Sub	75888	G=0.95413	A=0.04587
gnomAD - Genomes	African	Sub	41994	G=0.99200	A=0.00800
gnomAD - Genomes	American	Sub	13664	G=0.97541	A=0.02459
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	G=0.9705	A=0.0295
gnomAD - Genomes	East Asian	Sub	3128	G=1.0000	A=0.0000
gnomAD - Genomes	Other	Sub	2154	G=0.9763	A=0.0237
Allele Frequency Aggregator	Total	Global	18890	G=0.96511	A=0.03489
Allele Frequency Aggregator	European	Sub	14286	G=0.95786	A=0.04214
Allele Frequency Aggregator	African	Sub	2946	G=0.9919	A=0.0081
Allele Frequency Aggregator	Other	Sub	692	G=0.981	A=0.019
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.974	A=0.026
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.973	A=0.027
Allele Frequency Aggregator	Asian	Sub	112	G=1.000	A=0.000
Allele Frequency Aggregator	South Asian	Sub	98	G=1.00	A=0.00
1000Genomes_30x	Global	Study-wide	6404	G=0.9869	A=0.0131
1000Genomes_30x	African	Sub	1786	G=0.9961	A=0.0039
1000Genomes_30x	Europe	Sub	1266	G=0.9581	A=0.0419
1000Genomes_30x	South Asian	Sub	1202	G=0.9967	A=0.0033
1000Genomes_30x	East Asian	Sub	1170	G=1.0000	A=0.0000
1000Genomes_30x	American	Sub	980	G=0.980	A=0.020
1000Genomes	Global	Study-wide	5008	G=0.9872	A=0.0128
1000Genomes	African	Sub	1322	G=0.9955	A=0.0045
1000Genomes	East Asian	Sub	1008	G=1.0000	A=0.0000
1000Genomes	Europe	Sub	1006	G=0.9612	A=0.0388
1000Genomes	South Asian	Sub	978	G=0.998	A=0.002
1000Genomes	American	Sub	694	G=0.976	A=0.024
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.9667	A=0.0333
Korean Genome Project	KOREAN	Study-wide	1832	G=0.9989	A=0.0011
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.966	A=0.034
Northern Sweden	ACPOP	Study-wide	600	G=0.968	A=0.032
Qatari	Global	Study-wide	216	G=0.986	A=0.014
The Danish reference pan genome	Danish	Study-wide	40	G=0.88	A=0.12
SGDP_PRJ	Global	Study-wide	8	G=0.5	A=0.5
Siberian	Global	Study-wide	2	G=0.5	A=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 19	NC_000019.10:g.4060775G>A
GRCh37.p13 chr 19	NC_000019.9:g.4060773G>A

Gene: ZBTB7A, zinc finger and BTB domain containing 7A (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ZBTB7A transcript variant 2	NM_001317990.2:c.-16+4655… NM_001317990.2:c.-16+4655C>T	N/A	Intron Variant
ZBTB7A transcript variant 1	NM_015898.4:c.-15-5528C>T	N/A	Intron Variant
ZBTB7A transcript variant X2	XM_005259571.5:c.-16+3473… XM_005259571.5:c.-16+3473C>T	N/A	Intron Variant
ZBTB7A transcript variant X1	XM_005259570.6:c.	N/A	Genic 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	G=	A
GRCh38.p14 chr 19	NC_000019.10:g.4060775=	NC_000019.10:g.4060775G>A
GRCh37.p13 chr 19	NC_000019.9:g.4060773=	NC_000019.9:g.4060773G>A
ZBTB7A transcript variant 2	NM_001317990.2:c.-16+4655=	NM_001317990.2:c.-16+4655C>T
ZBTB7A transcript	NM_015898.2:c.-15-5528=	NM_015898.2:c.-15-5528C>T
ZBTB7A transcript variant 1	NM_015898.4:c.-15-5528=	NM_015898.4:c.-15-5528C>T
ZBTB7A transcript variant X2	XM_005259571.1:c.-16+3473=	XM_005259571.1:c.-16+3473C>T
ZBTB7A transcript variant X2	XM_005259571.5:c.-16+3473=	XM_005259571.5:c.-16+3473C>T
ZBTB7A transcript variant X3	XM_005259572.1:c.-16+4655=	XM_005259572.1:c.-16+4655C>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#.

29 SubSNP, 13 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss237584373	Jul 15, 2010 (132)
2	EVA-GONL	ss994032645	Aug 21, 2014 (142)
3	1000GENOMES	ss1362145956	Aug 21, 2014 (142)
4	EVA_GENOME_DK	ss1578533736	Apr 01, 2015 (144)
5	EVA_DECODE	ss1698094897	Apr 01, 2015 (144)
6	WEILL_CORNELL_DGM	ss1937511367	Feb 12, 2016 (147)
7	JJLAB	ss2029530665	Sep 14, 2016 (149)
8	USC_VALOUEV	ss2158045598	Dec 20, 2016 (150)
9	HUMAN_LONGEVITY	ss2223874072	Dec 20, 2016 (150)
10	GNOMAD	ss2959850373	Nov 08, 2017 (151)
11	SWEGEN	ss3016999498	Nov 08, 2017 (151)
12	CSHL	ss3352170749	Nov 08, 2017 (151)
13	URBANLAB	ss3650856320	Oct 12, 2018 (152)
14	EGCUT_WGS	ss3683845011	Jul 13, 2019 (153)
15	EVA_DECODE	ss3702231145	Jul 13, 2019 (153)
16	ACPOP	ss3742805718	Jul 13, 2019 (153)
17	KHV_HUMAN_GENOMES	ss3821001520	Jul 13, 2019 (153)
18	EVA	ss3835321692	Apr 27, 2020 (154)
19	SGDP_PRJ	ss3887642782	Apr 27, 2020 (154)
20	KOGIC	ss3980702866	Apr 27, 2020 (154)
21	TOPMED	ss5066286685	Apr 26, 2021 (155)
22	1000G_HIGH_COVERAGE	ss5306294144	Oct 16, 2022 (156)
23	EVA	ss5433237774	Oct 16, 2022 (156)
24	HUGCELL_USP	ss5498951832	Oct 16, 2022 (156)
25	1000G_HIGH_COVERAGE	ss5611618158	Oct 16, 2022 (156)
26	SANFORD_IMAGENETICS	ss5661868305	Oct 16, 2022 (156)
27	EVA	ss5840178474	Oct 16, 2022 (156)
28	EVA	ss5927091741	Oct 16, 2022 (156)
29	EVA	ss5953296123	Oct 16, 2022 (156)
30	1000Genomes	NC_000019.9 - 4060773	Oct 12, 2018 (152)
31	1000Genomes_30x	NC_000019.10 - 4060775	Oct 16, 2022 (156)
32	Genetic variation in the Estonian population	NC_000019.9 - 4060773	Oct 12, 2018 (152)
33	The Danish reference pan genome	NC_000019.9 - 4060773	Apr 27, 2020 (154)
34	gnomAD - Genomes	NC_000019.10 - 4060775	Apr 26, 2021 (155)
35	Genome of the Netherlands Release 5	NC_000019.9 - 4060773	Apr 27, 2020 (154)
36	Korean Genome Project	NC_000019.10 - 4060775	Apr 27, 2020 (154)
37	Northern Sweden	NC_000019.9 - 4060773	Jul 13, 2019 (153)
38	Qatari	NC_000019.9 - 4060773	Apr 27, 2020 (154)
39	SGDP_PRJ	NC_000019.9 - 4060773	Apr 27, 2020 (154)
40	Siberian	NC_000019.9 - 4060773	Apr 27, 2020 (154)
41	TopMed	NC_000019.10 - 4060775	Apr 26, 2021 (155)
42	ALFA	NC_000019.10 - 4060775	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
ss1698094897	NC_000019.8:4011772:G:A	NC_000019.10:4060774:G:A	(self)
75515159, 29583259, 4720540, 18644515, 16090583, 19553289, 39659762, 10561952, ss237584373, ss994032645, ss1362145956, ss1578533736, ss1937511367, ss2029530665, ss2158045598, ss2959850373, ss3016999498, ss3352170749, ss3683845011, ss3742805718, ss3835321692, ss3887642782, ss5433237774, ss5661868305, ss5840178474, ss5953296123	NC_000019.9:4060772:G:A	NC_000019.10:4060774:G:A	(self)
99144093, 532552126, 37080867, 281832349, 11590856825, ss2223874072, ss3650856320, ss3702231145, ss3821001520, ss3980702866, ss5066286685, ss5306294144, ss5498951832, ss5611618158, ss5927091741	NC_000019.10:4060774:G:A	NC_000019.10:4060774:G:A	(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 rs79027258

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

rs79027258