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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.

rs1490568978

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr9:41133719 (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=0.00000 (0/11862, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CBWD6 : Synonymous 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 11862 G=1.00000 A=0.00000 1.0 0.0 0.0 N/A
European Sub 7618 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Sub 2816 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 2708 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 146 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 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 470 G=1.000 A=0.000 1.0 0.0 0.0 N/A


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
Allele Frequency Aggregator Total Global 11862 G=1.00000 A=0.00000
Allele Frequency Aggregator European Sub 7618 G=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 2816 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000
Allele Frequency Aggregator Other Sub 470 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 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 9 NC_000009.12:g.41133719G>A
GRCh37.p13 chr 9 NC_000009.11:g.69206948G>A
Gene: CBWD6, COBW domain containing 6 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ZNG1F transcript variant 1 NM_001085457.2:c.840C>T D [GAC] > D [GAT] Coding Sequence Variant
zinc-regulated GTPase metalloprotein activator 1F isoform 1 NP_001078926.1:p.Asp280= D (Asp) > D (Asp) Synonymous Variant
ZNG1F transcript variant 2 NM_001386876.1:c.780C>T D [GAC] > D [GAT] Coding Sequence Variant
zinc-regulated GTPase metalloprotein activator 1F isoform 2 NP_001373805.1:p.Asp260= D (Asp) > D (Asp) Synonymous Variant
ZNG1F transcript variant 3 NM_001386877.1:c.693C>T D [GAC] > D [GAT] Coding Sequence Variant
zinc-regulated GTPase metalloprotein activator 1F isoform 3 NP_001373806.1:p.Asp231= D (Asp) > D (Asp) Synonymous Variant
ZNG1F transcript variant 4 NR_170339.1:n.875C>T N/A Non Coding Transcript Variant
ZNG1F transcript variant X9 XM_017015027.2:c. N/A Genic Downstream Transcript Variant
ZNG1F transcript variant X13 XM_017015030.2:c. N/A Genic Downstream Transcript Variant
ZNG1F transcript variant X14 XM_017015031.1:c.381C>T D [GAC] > D [GAT] Coding Sequence Variant
zinc-regulated GTPase metalloprotein activator 1F isoform X13 XP_016870520.1:p.Asp127= D (Asp) > D (Asp) Synonymous Variant
ZNG1F transcript variant X20 XM_017015033.1:c.294C>T D [GAC] > D [GAT] Coding Sequence Variant
zinc-regulated GTPase metalloprotein activator 1F isoform X16 XP_016870522.1:p.Asp98= D (Asp) > D (Asp) Synonymous Variant
ZNG1F transcript variant X22 XM_017015034.1:c.42C>T D [GAC] > D [GAT] Coding Sequence Variant
zinc-regulated GTPase metalloprotein activator 1F isoform X17 XP_016870523.1:p.Asp14= D (Asp) > D (Asp) Synonymous Variant
ZNG1F transcript variant X15 XM_024447652.1:c.336C>T D [GAC] > D [GAT] Coding Sequence Variant
zinc-regulated GTPase metalloprotein activator 1F isoform X14 XP_024303420.1:p.Asp112= D (Asp) > D (Asp) Synonymous Variant
ZNG1F transcript variant X1 XM_017015019.2:c.825C>T D [GAC] > D [GAT] Coding Sequence Variant
zinc-regulated GTPase metalloprotein activator 1F isoform X1 XP_016870508.1:p.Asp275= D (Asp) > D (Asp) Synonymous Variant
ZNG1F transcript variant X2 XM_017015021.2:c.768C>T D [GAC] > D [GAT] Coding Sequence Variant
zinc-regulated GTPase metalloprotein activator 1F isoform X2 XP_016870510.1:p.Asp256= D (Asp) > D (Asp) Synonymous Variant
ZNG1F transcript variant X3 XM_017015022.2:c.738C>T D [GAC] > D [GAT] Coding Sequence Variant
zinc-regulated GTPase metalloprotein activator 1F isoform X3 XP_016870511.1:p.Asp246= D (Asp) > D (Asp) Synonymous Variant
ZNG1F transcript variant X4 XM_017015023.2:c.723C>T D [GAC] > D [GAT] Coding Sequence Variant
zinc-regulated GTPase metalloprotein activator 1F isoform X4 XP_016870512.1:p.Asp241= D (Asp) > D (Asp) Synonymous Variant
ZNG1F transcript variant X5 XM_017015025.2:c.681C>T D [GAC] > D [GAT] Coding Sequence Variant
zinc-regulated GTPase metalloprotein activator 1F isoform X5 XP_016870514.1:p.Asp227= D (Asp) > D (Asp) Synonymous Variant
ZNG1F transcript variant X6 XM_047423720.1:c.636C>T D [GAC] > D [GAT] Coding Sequence Variant
zinc-regulated GTPase metalloprotein activator 1F isoform X6 XP_047279676.1:p.Asp212= D (Asp) > D (Asp) Synonymous Variant
ZNG1F transcript variant X7 XM_017015026.2:c.825C>T D [GAC] > D [GAT] Coding Sequence Variant
zinc-regulated GTPase metalloprotein activator 1F isoform X7 XP_016870515.1:p.Asp275= D (Asp) > D (Asp) Synonymous Variant
ZNG1F transcript variant X8 XM_047423721.1:c.780C>T D [GAC] > D [GAT] Coding Sequence Variant
zinc-regulated GTPase metalloprotein activator 1F isoform X8 XP_047279677.1:p.Asp260= D (Asp) > D (Asp) Synonymous Variant
ZNG1F transcript variant X10 XM_047423722.1:c.456C>T D [GAC] > D [GAT] Coding Sequence Variant
zinc-regulated GTPase metalloprotein activator 1F isoform X10 XP_047279678.1:p.Asp152= D (Asp) > D (Asp) Synonymous Variant
ZNG1F transcript variant X11 XM_017015028.2:c.456C>T D [GAC] > D [GAT] Coding Sequence Variant
zinc-regulated GTPase metalloprotein activator 1F isoform X10 XP_016870517.1:p.Asp152= D (Asp) > D (Asp) Synonymous Variant
ZNG1F transcript variant X12 XM_017015029.3:c.441C>T D [GAC] > D [GAT] Coding Sequence Variant
zinc-regulated GTPase metalloprotein activator 1F isoform X11 XP_016870518.1:p.Asp147= D (Asp) > D (Asp) Synonymous Variant
ZNG1F transcript variant X19 XM_047423723.1:c.297C>T D [GAC] > D [GAT] Coding Sequence Variant
zinc-regulated GTPase metalloprotein activator 1F isoform X15 XP_047279679.1:p.Asp99= D (Asp) > D (Asp) Synonymous Variant
ZNG1F transcript variant X23 XM_017015035.2:c.783C>T D [GAC] > D [GAT] Coding Sequence Variant
zinc-regulated GTPase metalloprotein activator 1F isoform X18 XP_016870524.1:p.Asp261= D (Asp) > D (Asp) Synonymous Variant
ZNG1F transcript variant X24 XM_024447653.2:c.753C>T D [GAC] > D [GAT] Coding Sequence Variant
zinc-regulated GTPase metalloprotein activator 1F isoform X19 XP_024303421.1:p.Asp251= D (Asp) > D (Asp) Synonymous Variant
ZNG1F transcript variant X25 XM_017015036.2:c.696C>T D [GAC] > D [GAT] Coding Sequence Variant
zinc-regulated GTPase metalloprotein activator 1F isoform X20 XP_016870525.1:p.Asp232= D (Asp) > D (Asp) Synonymous Variant
ZNG1F transcript variant X16 XR_001746359.2:n. N/A Genic Downstream Transcript Variant
ZNG1F transcript variant X18 XR_001746361.2:n. N/A Genic Downstream Transcript Variant
ZNG1F transcript variant X21 XR_001746362.2:n. N/A Genic Downstream Transcript Variant
ZNG1F transcript variant X17 XR_007061337.1:n. N/A Genic Downstream Transcript 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 9 NC_000009.12:g.41133719= NC_000009.12:g.41133719G>A
GRCh37.p13 chr 9 NC_000009.11:g.69206948= NC_000009.11:g.69206948G>A
ZNG1F transcript variant X12 XM_017015029.3:c.441= XM_017015029.3:c.441C>T
CBWD6 transcript variant X11 XM_017015029.2:c.441= XM_017015029.2:c.441C>T
CBWD6 transcript variant X11 XM_017015029.1:c.441= XM_017015029.1:c.441C>T
ZNG1F transcript variant X11 XM_017015028.2:c.456= XM_017015028.2:c.456C>T
CBWD6 transcript variant X10 XM_017015028.1:c.456= XM_017015028.1:c.456C>T
ZNG1F transcript variant 1 NM_001085457.2:c.840= NM_001085457.2:c.840C>T
CBWD6 transcript NM_001085457.1:c.840= NM_001085457.1:c.840C>T
ZNG1F transcript variant X1 XM_017015019.2:c.825= XM_017015019.2:c.825C>T
CBWD6 transcript variant X1 XM_017015019.1:c.825= XM_017015019.1:c.825C>T
ZNG1F transcript variant X23 XM_017015035.2:c.783= XM_017015035.2:c.783C>T
CBWD6 transcript variant X23 XM_017015035.1:c.783= XM_017015035.1:c.783C>T
ZNG1F transcript variant X2 XM_017015021.2:c.768= XM_017015021.2:c.768C>T
CBWD6 transcript variant X3 XM_017015021.1:c.768= XM_017015021.1:c.768C>T
ZNG1F transcript variant X24 XM_024447653.2:c.753= XM_024447653.2:c.753C>T
CBWD6 transcript variant X24 XM_024447653.1:c.753= XM_024447653.1:c.753C>T
ZNG1F transcript variant X3 XM_017015022.2:c.738= XM_017015022.2:c.738C>T
CBWD6 transcript variant X4 XM_017015022.1:c.738= XM_017015022.1:c.738C>T
ZNG1F transcript variant X4 XM_017015023.2:c.723= XM_017015023.2:c.723C>T
CBWD6 transcript variant X5 XM_017015023.1:c.723= XM_017015023.1:c.723C>T
ZNG1F transcript variant X25 XM_017015036.2:c.696= XM_017015036.2:c.696C>T
CBWD6 transcript variant X25 XM_017015036.1:c.696= XM_017015036.1:c.696C>T
ZNG1F transcript variant X7 XM_017015026.2:c.825= XM_017015026.2:c.825C>T
CBWD6 transcript variant X8 XM_017015026.1:c.825= XM_017015026.1:c.825C>T
ZNG1F transcript variant X5 XM_017015025.2:c.681= XM_017015025.2:c.681C>T
CBWD6 transcript variant X7 XM_017015025.1:c.681= XM_017015025.1:c.681C>T
ZNG1F transcript variant X10 XM_047423722.1:c.456= XM_047423722.1:c.456C>T
ZNG1F transcript variant 4 NR_170339.1:n.875= NR_170339.1:n.875C>T
ZNG1F transcript variant 2 NM_001386876.1:c.780= NM_001386876.1:c.780C>T
ZNG1F transcript variant 3 NM_001386877.1:c.693= NM_001386877.1:c.693C>T
ZNG1F transcript variant X8 XM_047423721.1:c.780= XM_047423721.1:c.780C>T
ZNG1F transcript variant X6 XM_047423720.1:c.636= XM_047423720.1:c.636C>T
ZNG1F transcript variant X19 XM_047423723.1:c.297= XM_047423723.1:c.297C>T
ZNG1F transcript variant X14 XM_017015031.1:c.381= XM_017015031.1:c.381C>T
ZNG1F transcript variant X15 XM_024447652.1:c.336= XM_024447652.1:c.336C>T
ZNG1F transcript variant X20 XM_017015033.1:c.294= XM_017015033.1:c.294C>T
ZNG1F transcript variant X22 XM_017015034.1:c.42= XM_017015034.1:c.42C>T
LOC57397 transcript NM_020667.1:c.-34= NM_020667.1:c.-34C>T
zinc-regulated GTPase metalloprotein activator 1F isoform X11 XP_016870518.1:p.Asp147= XP_016870518.1:p.Asp147=
zinc-regulated GTPase metalloprotein activator 1F isoform X10 XP_016870517.1:p.Asp152= XP_016870517.1:p.Asp152=
zinc-regulated GTPase metalloprotein activator 1F isoform 1 NP_001078926.1:p.Asp280= NP_001078926.1:p.Asp280=
zinc-regulated GTPase metalloprotein activator 1F isoform X1 XP_016870508.1:p.Asp275= XP_016870508.1:p.Asp275=
zinc-regulated GTPase metalloprotein activator 1F isoform X18 XP_016870524.1:p.Asp261= XP_016870524.1:p.Asp261=
zinc-regulated GTPase metalloprotein activator 1F isoform X2 XP_016870510.1:p.Asp256= XP_016870510.1:p.Asp256=
zinc-regulated GTPase metalloprotein activator 1F isoform X19 XP_024303421.1:p.Asp251= XP_024303421.1:p.Asp251=
zinc-regulated GTPase metalloprotein activator 1F isoform X3 XP_016870511.1:p.Asp246= XP_016870511.1:p.Asp246=
zinc-regulated GTPase metalloprotein activator 1F isoform X4 XP_016870512.1:p.Asp241= XP_016870512.1:p.Asp241=
zinc-regulated GTPase metalloprotein activator 1F isoform X20 XP_016870525.1:p.Asp232= XP_016870525.1:p.Asp232=
zinc-regulated GTPase metalloprotein activator 1F isoform X7 XP_016870515.1:p.Asp275= XP_016870515.1:p.Asp275=
zinc-regulated GTPase metalloprotein activator 1F isoform X5 XP_016870514.1:p.Asp227= XP_016870514.1:p.Asp227=
zinc-regulated GTPase metalloprotein activator 1F isoform X10 XP_047279678.1:p.Asp152= XP_047279678.1:p.Asp152=
zinc-regulated GTPase metalloprotein activator 1F isoform 2 NP_001373805.1:p.Asp260= NP_001373805.1:p.Asp260=
zinc-regulated GTPase metalloprotein activator 1F isoform 3 NP_001373806.1:p.Asp231= NP_001373806.1:p.Asp231=
zinc-regulated GTPase metalloprotein activator 1F isoform X8 XP_047279677.1:p.Asp260= XP_047279677.1:p.Asp260=
zinc-regulated GTPase metalloprotein activator 1F isoform X6 XP_047279676.1:p.Asp212= XP_047279676.1:p.Asp212=
zinc-regulated GTPase metalloprotein activator 1F isoform X15 XP_047279679.1:p.Asp99= XP_047279679.1:p.Asp99=
zinc-regulated GTPase metalloprotein activator 1F isoform X13 XP_016870520.1:p.Asp127= XP_016870520.1:p.Asp127=
zinc-regulated GTPase metalloprotein activator 1F isoform X14 XP_024303420.1:p.Asp112= XP_024303420.1:p.Asp112=
zinc-regulated GTPase metalloprotein activator 1F isoform X16 XP_016870522.1:p.Asp98= XP_016870522.1:p.Asp98=
zinc-regulated GTPase metalloprotein activator 1F isoform X17 XP_016870523.1:p.Asp14= XP_016870523.1:p.Asp14=
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#.

1 Frequency submission
No Submitter Submission ID Date (Build)
1 ALFA NC_000009.12 - 41133719 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
10545402079 NC_000009.12:41133718:G:A NC_000009.12:41133718: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 rs1490568978

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