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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs104894514

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr16:88646131 (GRCh38.p7) 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 / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.00005 (7/155082, GnomAD)
T=0.00013 (16/125568, TOPMED)
A=0.0000 (1/30934, GnomAD) (+ 2 more)
T=0.0000 (1/30934, GnomAD)
A=0.000 (2/5008, 1000G)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CYBA : Missense Variant
Publications
2 citations
Genomic View
See rs on genome
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.p7 chr 16 NC_000016.10:g.88646131G>A
GRCh38.p7 chr 16 NC_000016.10:g.88646131G>T
GRCh37.p13 chr 16 NC_000016.9:g.88712539G>A
GRCh37.p13 chr 16 NC_000016.9:g.88712539G>T
CYBA RefSeqGene (LRG_52) NG_007291.1:g.9919C>T
CYBA RefSeqGene (LRG_52) NG_007291.1:g.9919C>A
Gene: CYBA, cytochrome b-245 alpha chain (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CYBA transcript NM_000101.3:c.354C>T S [AGC] > S [AGT] Coding Sequence Variant
cytochrome b-245 light chain NP_000092.2:p.Ser...

NP_000092.2:p.Ser118=

S (Ser) > S (Ser) Synonymous Variant
CYBA transcript NM_000101.3:c.354C>A S [AGC] > R [AGA] Coding Sequence Variant
cytochrome b-245 light chain NP_000092.2:p.Ser...

NP_000092.2:p.Ser118Arg

S (Ser) > R (Arg) Missense Variant
CYBA transcript variant X1 XM_011522905.2:c....

XM_011522905.2:c.354C>T

S [AGC] > S [AGT] Coding Sequence Variant
cytochrome b-245 light chain isoform X1 XP_011521207.1:p....

XP_011521207.1:p.Ser118=

S (Ser) > S (Ser) Synonymous Variant
CYBA transcript variant X1 XM_011522905.2:c....

XM_011522905.2:c.354C>A

S [AGC] > R [AGA] Coding Sequence Variant
cytochrome b-245 light chain isoform X1 XP_011521207.1:p....

XP_011521207.1:p.Ser118Arg

S (Ser) > 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.

Allele: T (allele ID: 17298 )
ClinVar Accession Disease Names Clinical Significance
RCV000002347.2 Granulomatous disease, chronic, autosomal recessive, cytochrome b-negative Pathogenic
RCV000059045.1 not provided Not-Provided
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
The Genome Aggregation Database Global Study-wide 155082 G=0.99994 A=0.00001, T=0.00005
The Genome Aggregation Database European Sub 75174 G=1.0000 A=0.0000, T=0.0000
The Genome Aggregation Database Asian Sub 34346 G=1.0000 A=0.0000, T=0.0000
The Genome Aggregation Database American Sub 25094 G=0.9997 A=0.0000, T=0.0003
The Genome Aggregation Database Ashkenazi Jewish Sub 8288 G=1.000 A=0.000, T=0.000
The Genome Aggregation Database African Sub 8220 G=1.000 A=0.000, T=0.000
The Genome Aggregation Database Other Sub 3960 G=1.000 A=0.000, T=0.000
Trans-Omics for Precision Medicine Global Study-wide 125568 G=0.99987 T=0.00013
The Genome Aggregation Database Global Study-wide 30934 G=0.9999 T=0.0000, A=0.0000
The Genome Aggregation Database European Sub 18482 G=0.9999 T=0.0001, A=0.0001
The Genome Aggregation Database African Sub 8712 G=1.000 T=0.000, A=0.000
The Genome Aggregation Database East Asian Sub 1620 G=1.000 T=0.000, A=0.000
The Genome Aggregation Database Other Sub 980 G=1.00 T=0.00, A=0.00
The Genome Aggregation Database American Sub 838 G=1.00 T=0.00, A=0.00
The Genome Aggregation Database Ashkenazi Jewish Sub 302 G=1.00 T=0.00, A=0.00
1000Genomes Global Study-wide 5008 G=1.000 A=0.000
1000Genomes African Sub 1322 G=1.000 A=0.000
1000Genomes East Asian Sub 1008 G=0.999 A=0.001
1000Genomes Europe Sub 1006 G=0.999 A=0.001
1000Genomes South Asian Sub 978 G=1.00 A=0.00
1000Genomes American Sub 694 G=1.00 A=0.00
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 T Note
GRCh38.p7 chr 16 NC_000016.10:g.88...

NC_000016.10:g.88646131G=

NC_000016.10:g.88...

NC_000016.10:g.88646131G>A

NC_000016.10:g.88...

NC_000016.10:g.88646131G>T

GRCh37.p13 chr 16 NC_000016.9:g.887...

NC_000016.9:g.88712539G=

NC_000016.9:g.887...

NC_000016.9:g.88712539G>A

NC_000016.9:g.887...

NC_000016.9:g.88712539G>T

CYBA RefSeqGene (LRG_52) NG_007291.1:g.9919C= NG_007291.1:g.991...

NG_007291.1:g.9919C>T

NG_007291.1:g.991...

NG_007291.1:g.9919C>A

CYBA transcript NM_000101.3:c.354C= NM_000101.3:c.354C>T NM_000101.3:c.354C>A
CYBA transcript variant X1 XM_011522905.2:c....

XM_011522905.2:c.354C=

XM_011522905.2:c....

XM_011522905.2:c.354C>T

XM_011522905.2:c....

XM_011522905.2:c.354C>A

cytochrome b-245 light chain NP_000092.2:p.Ser...

NP_000092.2:p.Ser118=

NP_000092.2:p.Ser...

NP_000092.2:p.Ser118=

NP_000092.2:p.Ser...

NP_000092.2:p.Ser118Arg

cytochrome b-245 light chain isoform X1 XP_011521207.1:p....

XP_011521207.1:p.Ser118=

XP_011521207.1:p....

XP_011521207.1:p.Ser118=

XP_011521207.1:p....

XP_011521207.1:p.Ser118Arg

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#.

4 Frequency, 14 SubSNP, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMICIA ss244239398 Aug 29, 2012 (137)
2 OMIM-CURATED-RECORDS ss253284339 Aug 18, 2010 (132)
3 1000GENOMES ss339486582 May 09, 2011 (134)
4 SWISSPROT ss469104498 Jul 28, 2011 (133)
5 1000GENOMES ss491110003 May 04, 2012 (137)
6 1000GENOMES ss1357505103 Aug 21, 2014 (142)
7 EVA_EXAC ss1692461922 Apr 01, 2015 (144)
8 EVA_EXAC ss1692461923 Apr 01, 2015 (144)
9 HUMAN_LONGEVITY ss2214710277 Dec 20, 2016 (150)
10 GNOMAD ss2742229434 Nov 08, 2017 (151)
11 GNOMAD ss2749620288 Nov 08, 2017 (151)
12 GNOMAD ss2946542003 Nov 08, 2017 (151)
13 TOPMED ss3254662642 Nov 08, 2017 (151)
14 TOPMED ss3254662643 Nov 08, 2017 (151)
15 1000Genomes NC_000016.9 - 88712539 Jul 20, 2018 (151)
16 The Genome Aggregation Database NC_000016.9 - 88712539 Jul 20, 2018 (151)
17 The Genome Aggregation Database NC_000016.9 - 88712539 Jul 20, 2018 (151)
18 Trans-Omics for Precision Medicine NC_000016.10 - 88646131 Jul 20, 2018 (151)
19 ClinVar RCV000002347.2 Jul 20, 2018 (151)
20 ClinVar RCV000059045.1 Jul 20, 2018 (151)
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
70704877, 80243530, 11244169, ss339486582, ss491110003, ss1357505103, ss1692461922, ss1692461923, ss2742229434, ss2749620288, ss2946542003 NC_000016.9:88712538:G= NC_000016.10:88646130:G= (self)
150824340, ss244239398, ss253284339, ss469104498, ss2214710277, ss3254662642, ss3254662643 NC_000016.10:88646130:G= NC_000016.10:88646130:G= (self)
70704877, 80243530, 11244169, ss339486582, ss491110003, ss1357505103, ss1692461923, ss2742229434, ss2749620288, ss2946542003 NC_000016.9:88712538:G>A NC_000016.10:88646130:G>A (self)
ss2214710277, ss3254662642 NC_000016.10:88646130:G>A NC_000016.10:88646130:G>A (self)
80243530, 11244169, ss1692461922, ss2742229434, ss2749620288, ss2946542003 NC_000016.9:88712538:G>T NC_000016.10:88646130:G>T (self)
RCV000002347.2, RCV000059045.1, 150824340, ss244239398, ss253284339, ss469104498, ss3254662643 NC_000016.10:88646130:G>T NC_000016.10:88646130:G>T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

2 citations for rs104894514
PMID Title Author Year Journal
2243141 Human neutrophil cytochrome b light chain (p22-phox). Gene structure, chromosomal location, and mutations in cytochrome-negative autosomal recessive chronic granulomatous disease. Dinauer MC et al. 1990 The Journal of clinical investigation
10910929 Molecular analysis of 9 new families with chronic granulomatous disease caused by mutations in CYBA, the gene encoding p22(phox). Rae J et al. 2000 Blood

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: 0.1.4.post833+d3ba21e