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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.

rs1458108700

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr7:99486913 (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=0.000015 (4/264690, TOPMED)
A=0.000004 (1/251406, GnomAD_exome)
A=0.000007 (1/140230, GnomAD) (+ 1 more)
A=0.00006 (2/33244, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ZNF789 : Missense Variant
ZNF394 : 3 Prime UTR 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 33244 G=0.99994 A=0.00006 0.99988 0.0 0.00012 0
European Sub 24516 G=0.99996 A=0.00004 0.999918 0.0 0.000082 0
African Sub 2836 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Others Sub 108 G=1.000 A=0.000 1.0 0.0 0.0 N/A
African American Sub 2728 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 G=1.000 A=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 500 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 628 G=1.000 A=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Sub 4562 G=0.9998 A=0.0002 0.999562 0.0 0.000438 0


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=0.999985 A=0.000015
gnomAD - Exomes Global Study-wide 251406 G=0.999996 A=0.000004
gnomAD - Exomes European Sub 135358 G=0.999993 A=0.000007
gnomAD - Exomes Asian Sub 49006 G=1.00000 A=0.00000
gnomAD - Exomes American Sub 34578 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 16252 G=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10078 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6134 G=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 140230 G=0.999993 A=0.000007
gnomAD - Genomes European Sub 75948 G=0.99999 A=0.00001
gnomAD - Genomes African Sub 42038 G=1.00000 A=0.00000
gnomAD - Genomes American Sub 13632 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2154 G=1.0000 A=0.0000
Allele Frequency Aggregator Total Global 33244 G=0.99994 A=0.00006
Allele Frequency Aggregator European Sub 24516 G=0.99996 A=0.00004
Allele Frequency Aggregator Other Sub 4562 G=0.9998 A=0.0002
Allele Frequency Aggregator African Sub 2836 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 628 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 108 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 94 G=1.00 A=0.00
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.99486913G>A
GRCh37.p13 chr 7 NC_000007.13:g.99084536G>A
Gene: ZNF394, zinc finger protein 394 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ZNF394 transcript variant 3 NM_001345968.2:c.*28= N/A 3 Prime UTR Variant
ZNF394 transcript variant 2 NM_001345967.2:c. N/A Genic Downstream Transcript Variant
ZNF394 transcript variant 1 NM_032164.4:c. N/A Genic Downstream Transcript Variant
Gene: ZNF789, zinc finger protein 789 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ZNF789 transcript variant 2 NM_001013258.2:c. N/A Genic Downstream Transcript Variant
ZNF789 transcript variant 5 NM_001351001.2:c. N/A Genic Downstream Transcript Variant
ZNF789 transcript variant 1 NM_213603.3:c.703G>A G [GGG] > R [AGG] Coding Sequence Variant
zinc finger protein 789 isoform 1 NP_998768.2:p.Gly235Arg G (Gly) > R (Arg) Missense Variant
ZNF789 transcript variant 4 NM_001351000.2:c.589G>A G [GGG] > R [AGG] Coding Sequence Variant
zinc finger protein 789 isoform 4 NP_001337929.1:p.Gly197Arg G (Gly) > R (Arg) Missense Variant
ZNF789 transcript variant 6 NM_001351002.2:c.418G>A G [GGG] > R [AGG] Coding Sequence Variant
zinc finger protein 789 isoform 6 NP_001337931.1:p.Gly140Arg G (Gly) > R (Arg) Missense Variant
ZNF789 transcript variant 7 NM_001351004.2:c.418G>A G [GGG] > R [AGG] Coding Sequence Variant
zinc finger protein 789 isoform 6 NP_001337933.1:p.Gly140Arg G (Gly) > R (Arg) Missense Variant
ZNF789 transcript variant 3 NM_001350999.2:c.652G>A G [GGG] > R [AGG] Coding Sequence Variant
zinc finger protein 789 isoform 3 NP_001337928.1:p.Gly218Arg G (Gly) > R (Arg) Missense Variant
ZNF789 transcript variant 8 NR_147001.2:n. N/A Genic Downstream Transcript Variant
ZNF789 transcript variant 9 NR_147002.2:n. N/A Genic Downstream Transcript Variant
ZNF789 transcript variant 10 NR_147003.2:n. N/A Genic Downstream Transcript Variant
ZNF789 transcript variant X9 XM_047420231.1:c. N/A Genic Downstream Transcript Variant
ZNF789 transcript variant X1 XM_017012018.2:c.703G>A G [GGG] > R [AGG] Coding Sequence Variant
zinc finger protein 789 isoform X1 XP_016867507.1:p.Gly235Arg G (Gly) > R (Arg) Missense Variant
ZNF789 transcript variant X2 XM_047420226.1:c.682G>A G [GGG] > R [AGG] Coding Sequence Variant
zinc finger protein 789 isoform X2 XP_047276182.1:p.Gly228Arg G (Gly) > R (Arg) Missense Variant
ZNF789 transcript variant X8 XM_047420227.1:c.682G>A G [GGG] > R [AGG] Coding Sequence Variant
zinc finger protein 789 isoform X2 XP_047276183.1:p.Gly228Arg G (Gly) > R (Arg) Missense Variant
ZNF789 transcript variant X3 XM_047420228.1:c.682G>A G [GGG] > R [AGG] Coding Sequence Variant
zinc finger protein 789 isoform X2 XP_047276184.1:p.Gly228Arg G (Gly) > R (Arg) Missense Variant
ZNF789 transcript variant X4 XM_047420229.1:c.652G>A G [GGG] > R [AGG] Coding Sequence Variant
zinc finger protein 789 isoform X3 XP_047276185.1:p.Gly218Arg G (Gly) > R (Arg) Missense Variant
ZNF789 transcript variant X5 XM_017012022.2:c.652G>A G [GGG] > R [AGG] Coding Sequence Variant
zinc finger protein 789 isoform X3 XP_016867511.1:p.Gly218Arg G (Gly) > R (Arg) Missense Variant
ZNF789 transcript variant X6 XM_047420230.1:c.418G>A G [GGG] > R [AGG] Coding Sequence Variant
zinc finger protein 789 isoform X4 XP_047276186.1:p.Gly140Arg G (Gly) > R (Arg) Missense Variant
ZNF789 transcript variant X7 XM_024446725.2:c.418G>A G [GGG] > R [AGG] Coding Sequence Variant
zinc finger protein 789 isoform X4 XP_024302493.1:p.Gly140Arg G (Gly) > R (Arg) Missense 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 7 NC_000007.14:g.99486913= NC_000007.14:g.99486913G>A
GRCh37.p13 chr 7 NC_000007.13:g.99084536= NC_000007.13:g.99084536G>A
ZNF789 transcript variant 1 NM_213603.3:c.703= NM_213603.3:c.703G>A
ZNF789 transcript variant 1 NM_213603.2:c.703= NM_213603.2:c.703G>A
ZNF789 transcript variant X7 XM_024446725.2:c.418= XM_024446725.2:c.418G>A
ZNF789 transcript variant X6 XM_024446725.1:c.418= XM_024446725.1:c.418G>A
ZNF789 transcript variant X5 XM_017012022.2:c.652= XM_017012022.2:c.652G>A
ZNF789 transcript variant X5 XM_017012022.1:c.652= XM_017012022.1:c.652G>A
ZNF789 transcript variant 7 NM_001351004.2:c.418= NM_001351004.2:c.418G>A
ZNF789 transcript variant 7 NM_001351004.1:c.418= NM_001351004.1:c.418G>A
ZNF789 transcript variant 6 NM_001351002.2:c.418= NM_001351002.2:c.418G>A
ZNF789 transcript variant 6 NM_001351002.1:c.418= NM_001351002.1:c.418G>A
ZNF789 transcript variant 3 NM_001350999.2:c.652= NM_001350999.2:c.652G>A
ZNF789 transcript variant 3 NM_001350999.1:c.652= NM_001350999.1:c.652G>A
ZNF789 transcript variant 4 NM_001351000.2:c.589= NM_001351000.2:c.589G>A
ZNF789 transcript variant 4 NM_001351000.1:c.589= NM_001351000.1:c.589G>A
ZNF789 transcript variant X1 XM_017012018.2:c.703= XM_017012018.2:c.703G>A
ZNF789 transcript variant X1 XM_017012018.1:c.703= XM_017012018.1:c.703G>A
ZNF394 transcript variant 3 NM_001345968.2:c.*28= NM_001345968.2:c.*28C>T
ZNF394 transcript variant 3 NM_001345968.1:c.*28= NM_001345968.1:c.*28C>T
ZNF789 transcript variant X6 XM_047420230.1:c.418= XM_047420230.1:c.418G>A
ZNF789 transcript variant X4 XM_047420229.1:c.652= XM_047420229.1:c.652G>A
ZNF789 transcript variant X2 XM_047420226.1:c.682= XM_047420226.1:c.682G>A
ZNF789 transcript variant X8 XM_047420227.1:c.682= XM_047420227.1:c.682G>A
ZNF789 transcript variant X3 XM_047420228.1:c.682= XM_047420228.1:c.682G>A
zinc finger protein 789 isoform 1 NP_998768.2:p.Gly235= NP_998768.2:p.Gly235Arg
zinc finger protein 789 isoform X4 XP_024302493.1:p.Gly140= XP_024302493.1:p.Gly140Arg
zinc finger protein 789 isoform X3 XP_016867511.1:p.Gly218= XP_016867511.1:p.Gly218Arg
zinc finger protein 789 isoform 6 NP_001337933.1:p.Gly140= NP_001337933.1:p.Gly140Arg
zinc finger protein 789 isoform 6 NP_001337931.1:p.Gly140= NP_001337931.1:p.Gly140Arg
zinc finger protein 789 isoform 3 NP_001337928.1:p.Gly218= NP_001337928.1:p.Gly218Arg
zinc finger protein 789 isoform 4 NP_001337929.1:p.Gly197= NP_001337929.1:p.Gly197Arg
zinc finger protein 789 isoform X1 XP_016867507.1:p.Gly235= XP_016867507.1:p.Gly235Arg
zinc finger protein 789 isoform X4 XP_047276186.1:p.Gly140= XP_047276186.1:p.Gly140Arg
zinc finger protein 789 isoform X3 XP_047276185.1:p.Gly218= XP_047276185.1:p.Gly218Arg
zinc finger protein 789 isoform X2 XP_047276182.1:p.Gly228= XP_047276182.1:p.Gly228Arg
zinc finger protein 789 isoform X2 XP_047276183.1:p.Gly228= XP_047276183.1:p.Gly228Arg
zinc finger protein 789 isoform X2 XP_047276184.1:p.Gly228= XP_047276184.1:p.Gly228Arg
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#.

3 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2736594882 Nov 08, 2017 (151)
2 GNOMAD ss4169374396 Apr 26, 2021 (155)
3 TOPMED ss4756521525 Apr 26, 2021 (155)
4 gnomAD - Genomes NC_000007.14 - 99486913 Apr 26, 2021 (155)
5 gnomAD - Exomes NC_000007.13 - 99084536 Jul 13, 2019 (153)
6 TopMed NC_000007.14 - 99486913 Apr 26, 2021 (155)
7 ALFA NC_000007.14 - 99486913 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
5759011, ss2736594882 NC_000007.13:99084535:G:A NC_000007.14:99486912:G:A (self)
270602127, 593899084, 7272916666, ss4169374396, ss4756521525 NC_000007.14:99486912:G:A NC_000007.14:99486912: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 rs1458108700

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.post820+afb47a3d