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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs148702080

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr7:99499935 (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>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.001696 (449/264690, TOPMED)
G=0.000562 (141/250954, GnomAD_exome)
G=0.001440 (202/140236, GnomAD) (+ 12 more)
G=0.000491 (59/120232, ExAC)
G=0.00025 (11/44758, ALFA)
G=0.00177 (23/13006, GO-ESP)
G=0.0014 (9/6404, 1000G_30x)
G=0.0012 (6/5008, 1000G)
G=0.0003 (1/3854, ALSPAC)
G=0.0003 (1/3708, TWINSUK)
G=0.001 (1/998, GoNL)
G=0.002 (1/534, MGP)
G=0.005 (1/216, Qatari)
A=0.5 (1/2, SGDP_PRJ)
G=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ZNF394 : Stop Gained
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 44758 A=0.99975 G=0.00025, T=0.00000
European Sub 32772 A=0.99982 G=0.00018, T=0.00000
African Sub 3558 A=0.9997 G=0.0003, T=0.0000
African Others Sub 122 A=1.000 G=0.000, T=0.000
African American Sub 3436 A=0.9997 G=0.0003, T=0.0000
Asian Sub 168 A=1.000 G=0.000, T=0.000
East Asian Sub 112 A=1.000 G=0.000, T=0.000
Other Asian Sub 56 A=1.00 G=0.00, T=0.00
Latin American 1 Sub 500 A=1.000 G=0.000, T=0.000
Latin American 2 Sub 626 A=1.000 G=0.000, T=0.000
South Asian Sub 98 A=1.00 G=0.00, T=0.00
Other Sub 7036 A=0.9994 G=0.0006, T=0.0000


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 A=0.998304 G=0.001696
gnomAD - Exomes Global Study-wide 250954 A=0.999438 G=0.000562
gnomAD - Exomes European Sub 134996 A=0.999852 G=0.000148
gnomAD - Exomes Asian Sub 48966 A=1.00000 G=0.00000
gnomAD - Exomes American Sub 34580 A=0.99861 G=0.00139
gnomAD - Exomes African Sub 16210 A=0.99574 G=0.00426
gnomAD - Exomes Ashkenazi Jewish Sub 10074 A=0.99990 G=0.00010
gnomAD - Exomes Other Sub 6128 A=0.9995 G=0.0005
gnomAD - Genomes Global Study-wide 140236 A=0.998560 G=0.001440
gnomAD - Genomes European Sub 75958 A=0.99987 G=0.00013
gnomAD - Genomes African Sub 42026 A=0.99645 G=0.00355
gnomAD - Genomes American Sub 13644 A=0.99736 G=0.00264
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.9997 G=0.0003
gnomAD - Genomes East Asian Sub 3134 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2150 A=0.9972 G=0.0028
ExAC Global Study-wide 120232 A=0.999509 G=0.000491
ExAC Europe Sub 72594 A=0.99983 G=0.00017
ExAC Asian Sub 24978 A=1.00000 G=0.00000
ExAC American Sub 11528 A=0.99939 G=0.00061
ExAC African Sub 10230 A=0.99609 G=0.00391
ExAC Other Sub 902 A=1.000 G=0.000
Allele Frequency Aggregator Total Global 44758 A=0.99975 G=0.00025, T=0.00000
Allele Frequency Aggregator European Sub 32772 A=0.99982 G=0.00018, T=0.00000
Allele Frequency Aggregator Other Sub 7036 A=0.9994 G=0.0006, T=0.0000
Allele Frequency Aggregator African Sub 3558 A=0.9997 G=0.0003, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 626 A=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 A=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 168 A=1.000 G=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 98 A=1.00 G=0.00, T=0.00
GO Exome Sequencing Project Global Study-wide 13006 A=0.99823 G=0.00177
GO Exome Sequencing Project European American Sub 8600 A=0.9997 G=0.0003
GO Exome Sequencing Project African American Sub 4406 A=0.9955 G=0.0045
1000Genomes_30x Global Study-wide 6404 A=0.9986 G=0.0014
1000Genomes_30x African Sub 1786 A=0.9961 G=0.0039
1000Genomes_30x Europe Sub 1266 A=0.9992 G=0.0008
1000Genomes_30x South Asian Sub 1202 A=1.0000 G=0.0000
1000Genomes_30x East Asian Sub 1170 A=1.0000 G=0.0000
1000Genomes_30x American Sub 980 A=0.999 G=0.001
1000Genomes Global Study-wide 5008 A=0.9988 G=0.0012
1000Genomes African Sub 1322 A=0.9970 G=0.0030
1000Genomes East Asian Sub 1008 A=1.0000 G=0.0000
1000Genomes Europe Sub 1006 A=0.9990 G=0.0010
1000Genomes South Asian Sub 978 A=1.000 G=0.000
1000Genomes American Sub 694 A=0.999 G=0.001
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9997 G=0.0003
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9997 G=0.0003
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.999 G=0.001
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.998 G=0.002
Qatari Global Study-wide 216 A=0.995 G=0.005
SGDP_PRJ Global Study-wide 2 A=0.5 G=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 7 NC_000007.14:g.99499935A>G
GRCh38.p14 chr 7 NC_000007.14:g.99499935A>T
GRCh37.p13 chr 7 NC_000007.13:g.99097558A>G
GRCh37.p13 chr 7 NC_000007.13:g.99097558A>T
Gene: ZNF394, zinc finger protein 394 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ZNF394 transcript variant 1 NM_032164.4:c.159T>C Y [TAT] > Y [TAC] Coding Sequence Variant
zinc finger protein 394 isoform 1 NP_115540.2:p.Tyr53= Y (Tyr) > Y (Tyr) Synonymous Variant
ZNF394 transcript variant 1 NM_032164.4:c.159T>A Y [TAT] > * [TAA] Coding Sequence Variant
zinc finger protein 394 isoform 1 NP_115540.2:p.Tyr53Ter Y (Tyr) > * (Ter) Stop Gained
ZNF394 transcript variant 2 NM_001345967.2:c.159T>C Y [TAT] > Y [TAC] Coding Sequence Variant
zinc finger protein 394 isoform 2 NP_001332896.1:p.Tyr53= Y (Tyr) > Y (Tyr) Synonymous Variant
ZNF394 transcript variant 2 NM_001345967.2:c.159T>A Y [TAT] > * [TAA] Coding Sequence Variant
zinc finger protein 394 isoform 2 NP_001332896.1:p.Tyr53Ter Y (Tyr) > * (Ter) Stop Gained
ZNF394 transcript variant 3 NM_001345968.2:c.159T>C Y [TAT] > Y [TAC] Coding Sequence Variant
zinc finger protein 394 isoform 3 NP_001332897.1:p.Tyr53= Y (Tyr) > Y (Tyr) Synonymous Variant
ZNF394 transcript variant 3 NM_001345968.2:c.159T>A Y [TAT] > * [TAA] Coding Sequence Variant
zinc finger protein 394 isoform 3 NP_001332897.1:p.Tyr53Ter Y (Tyr) > * (Ter) Stop Gained
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 A= G T
GRCh38.p14 chr 7 NC_000007.14:g.99499935= NC_000007.14:g.99499935A>G NC_000007.14:g.99499935A>T
GRCh37.p13 chr 7 NC_000007.13:g.99097558= NC_000007.13:g.99097558A>G NC_000007.13:g.99097558A>T
ZNF394 transcript variant 1 NM_032164.4:c.159= NM_032164.4:c.159T>C NM_032164.4:c.159T>A
ZNF394 transcript variant 1 NM_032164.3:c.159= NM_032164.3:c.159T>C NM_032164.3:c.159T>A
ZNF394 transcript NM_032164.2:c.159= NM_032164.2:c.159T>C NM_032164.2:c.159T>A
ZNF394 transcript variant 2 NM_001345967.2:c.159= NM_001345967.2:c.159T>C NM_001345967.2:c.159T>A
ZNF394 transcript variant 2 NM_001345967.1:c.159= NM_001345967.1:c.159T>C NM_001345967.1:c.159T>A
ZNF394 transcript variant 3 NM_001345968.2:c.159= NM_001345968.2:c.159T>C NM_001345968.2:c.159T>A
ZNF394 transcript variant 3 NM_001345968.1:c.159= NM_001345968.1:c.159T>C NM_001345968.1:c.159T>A
zinc finger protein 394 isoform 1 NP_115540.2:p.Tyr53= NP_115540.2:p.Tyr53= NP_115540.2:p.Tyr53Ter
zinc finger protein 394 isoform 2 NP_001332896.1:p.Tyr53= NP_001332896.1:p.Tyr53= NP_001332896.1:p.Tyr53Ter
zinc finger protein 394 isoform 3 NP_001332897.1:p.Tyr53= NP_001332897.1:p.Tyr53= NP_001332897.1:p.Tyr53Ter
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, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342240640 May 09, 2011 (134)
2 1000GENOMES ss488868136 May 04, 2012 (137)
3 CLINSEQ_SNP ss491910445 May 04, 2012 (137)
4 EVA-GONL ss984589286 Aug 21, 2014 (142)
5 1000GENOMES ss1326333719 Aug 21, 2014 (142)
6 EVA_UK10K_ALSPAC ss1618796948 Apr 01, 2015 (144)
7 EVA_UK10K_TWINSUK ss1661790981 Apr 01, 2015 (144)
8 EVA_EXAC ss1688839198 Apr 01, 2015 (144)
9 EVA_MGP ss1711173064 Apr 01, 2015 (144)
10 WEILL_CORNELL_DGM ss1927850361 Feb 12, 2016 (147)
11 HUMAN_LONGEVITY ss2296192568 Dec 20, 2016 (150)
12 GNOMAD ss2736595527 Nov 08, 2017 (151)
13 GNOMAD ss2747870853 Nov 08, 2017 (151)
14 GNOMAD ss2856752423 Nov 08, 2017 (151)
15 EVA ss3824296019 Apr 26, 2020 (154)
16 EVA ss3825724358 Apr 26, 2020 (154)
17 SGDP_PRJ ss3867979700 Apr 26, 2020 (154)
18 FSA-LAB ss3984373717 Apr 26, 2021 (155)
19 TOPMED ss4756524615 Apr 26, 2021 (155)
20 1000G_HIGH_COVERAGE ss5274028314 Oct 17, 2022 (156)
21 EVA ss5375489870 Oct 17, 2022 (156)
22 HUGCELL_USP ss5470999794 Oct 17, 2022 (156)
23 1000G_HIGH_COVERAGE ss5562807431 Oct 17, 2022 (156)
24 EVA ss5860083189 Oct 17, 2022 (156)
25 EVA ss5972769660 Oct 17, 2022 (156)
26 1000Genomes NC_000007.13 - 99097558 Oct 12, 2018 (152)
27 1000Genomes_30x NC_000007.14 - 99499935 Oct 17, 2022 (156)
28 The Avon Longitudinal Study of Parents and Children NC_000007.13 - 99097558 Oct 12, 2018 (152)
29 ExAC NC_000007.13 - 99097558 Oct 12, 2018 (152)
30 gnomAD - Genomes NC_000007.14 - 99499935 Apr 26, 2021 (155)
31 gnomAD - Exomes NC_000007.13 - 99097558 Jul 13, 2019 (153)
32 GO Exome Sequencing Project NC_000007.13 - 99097558 Oct 12, 2018 (152)
33 Genome of the Netherlands Release 5 NC_000007.13 - 99097558 Apr 26, 2020 (154)
34 Medical Genome Project healthy controls from Spanish population NC_000007.13 - 99097558 Apr 26, 2020 (154)
35 Qatari NC_000007.13 - 99097558 Apr 26, 2020 (154)
36 SGDP_PRJ NC_000007.13 - 99097558 Apr 26, 2020 (154)
37 TopMed NC_000007.14 - 99499935 Apr 26, 2021 (155)
38 UK 10K study - Twins NC_000007.13 - 99097558 Oct 12, 2018 (152)
39 ALFA NC_000007.14 - 99499935 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
ss491910445 NC_000007.12:98935493:A:G NC_000007.14:99499934:A:G (self)
38347485, 21338353, 8912856, 5759718, 753963, 9526170, 288824, 9892291, 19996680, 21338353, ss342240640, ss488868136, ss984589286, ss1326333719, ss1618796948, ss1661790981, ss1688839198, ss1711173064, ss1927850361, ss2736595527, ss2747870853, ss2856752423, ss3824296019, ss3825724358, ss3867979700, ss3984373717, ss5375489870, ss5972769660 NC_000007.13:99097557:A:G NC_000007.14:99499934:A:G (self)
50333366, 270605233, 593902174, 5722699676, ss2296192568, ss4756524615, ss5274028314, ss5470999794, ss5562807431, ss5860083189 NC_000007.14:99499934:A:G NC_000007.14:99499934:A:G (self)
5722699676 NC_000007.14:99499934:A:T NC_000007.14:99499934:A:T (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 rs148702080

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