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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.

rs104894309

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr11:112086940 (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
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.00000 (1/246150, GnomAD)
T=0.00001 (1/121214, ExAC)
Clinical Significance
Reported in ClinVar
Gene : Consequence
SDHD : Stop Gained
TIMM8B : 2KB Upstream Variant
Publications
1 citation
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 11 NC_000011.10:g.112086940C>A
GRCh38.p7 chr 11 NC_000011.10:g.112086940C>T
GRCh37.p13 chr 11 NC_000011.9:g.111957664C>A
GRCh37.p13 chr 11 NC_000011.9:g.111957664C>T
SDHD RefSeqGene NG_012337.3:g.5094C>A
SDHD RefSeqGene NG_012337.3:g.5094C>T
TIMM8B RefSeqGene NG_033145.1:g.4859G>T
TIMM8B RefSeqGene NG_033145.1:g.4859G>A
Gene: TIMM8B, translocase of inner mitochondrial membrane 8 homolog B (yeast) (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
TIMM8B transcript variant 1 NM_012459.2:c. N/A Upstream Transcript Variant
TIMM8B transcript variant 2 NR_028383.1:n. N/A Upstream Transcript Variant
Gene: SDHD, succinate dehydrogenase complex subunit D (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SDHD transcript variant 1 NM_003002.3:c.33C>A C [TGC] > * [TGA] Coding Sequence Variant
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial isoform a precursor NP_002993.1:p.Cys...

NP_002993.1:p.Cys11Ter

C (Cys) > * (Ter) Stop Gained
SDHD transcript variant 1 NM_003002.3:c.33C>T C [TGC] > C [TGT] Coding Sequence Variant
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial isoform a precursor NP_002993.1:p.Cys11= C (Cys) > C (Cys) Synonymous Variant
SDHD transcript variant 2 NM_001276503.1:c....

NM_001276503.1:c.33C>A

C [TGC] > * [TGA] Coding Sequence Variant
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial isoform b precursor NP_001263432.1:p....

NP_001263432.1:p.Cys11Ter

C (Cys) > * (Ter) Stop Gained
SDHD transcript variant 2 NM_001276503.1:c....

NM_001276503.1:c.33C>T

C [TGC] > C [TGT] Coding Sequence Variant
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial isoform b precursor NP_001263432.1:p....

NP_001263432.1:p.Cys11=

C (Cys) > C (Cys) Synonymous Variant
SDHD transcript variant 3 NM_001276504.1:c....

NM_001276504.1:c.33C>A

C [TGC] > * [TGA] Coding Sequence Variant
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial isoform c precursor NP_001263433.1:p....

NP_001263433.1:p.Cys11Ter

C (Cys) > * (Ter) Stop Gained
SDHD transcript variant 3 NM_001276504.1:c....

NM_001276504.1:c.33C>T

C [TGC] > C [TGT] Coding Sequence Variant
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial isoform c precursor NP_001263433.1:p....

NP_001263433.1:p.Cys11=

C (Cys) > C (Cys) Synonymous Variant
SDHD transcript variant 4 NM_001276506.1:c....

NM_001276506.1:c.33C>A

C [TGC] > * [TGA] Coding Sequence Variant
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial isoform d precursor NP_001263435.1:p....

NP_001263435.1:p.Cys11Ter

C (Cys) > * (Ter) Stop Gained
SDHD transcript variant 4 NM_001276506.1:c....

NM_001276506.1:c.33C>T

C [TGC] > C [TGT] Coding Sequence Variant
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial isoform d precursor NP_001263435.1:p....

NP_001263435.1:p.Cys11=

C (Cys) > C (Cys) Synonymous Variant
SDHD transcript variant 5 NR_077060.1:n.117C>A N/A Non Coding Transcript Variant
SDHD transcript variant 5 NR_077060.1:n.117C>T N/A Non Coding 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.

Allele: A (allele ID: 21954 )
ClinVar Accession Disease Names Clinical Significance
RCV000007324.2 Pheochromocytoma Pathogenic
RCV000221327.2 Hereditary cancer-predisposing syndrome Pathogenic
RCV000529506.1 Paragangliomas 1 Pathogenic
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 246150 C=1.00000 T=0.00000
The Genome Aggregation Database European Sub 133912 C=1.00000 T=0.00000
The Genome Aggregation Database Asian Sub 48028 C=1.0000 T=0.0000
The Genome Aggregation Database American Sub 33574 C=1.0000 T=0.0000
The Genome Aggregation Database African Sub 15302 C=1.0000 T=0.0000
The Genome Aggregation Database Ashkenazi Jewish Sub 9850 C=1.000 T=0.000
The Genome Aggregation Database Other Sub 5484 C=1.000 T=0.000
The Exome Aggregation Consortium Global Study-wide 121214 C=0.99999 T=0.00001
The Exome Aggregation Consortium Europe Sub 73214 C=1.0000 T=0.0000
The Exome Aggregation Consortium Asian Sub 25152 C=1.0000 T=0.0000
The Exome Aggregation Consortium American Sub 11552 C=1.0000 T=0.0000
The Exome Aggregation Consortium African Sub 10398 C=1.0000 T=0.0000
The Exome Aggregation Consortium Other Sub 898 C=1.00 T=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 C= A T Note
GRCh38.p7 chr 11 NC_000011.10:g.11...

NC_000011.10:g.112086940C=

NC_000011.10:g.11...

NC_000011.10:g.112086940C>A

NC_000011.10:g.11...

NC_000011.10:g.112086940C>T

GRCh37.p13 chr 11 NC_000011.9:g.111...

NC_000011.9:g.111957664C=

NC_000011.9:g.111...

NC_000011.9:g.111957664C>A

NC_000011.9:g.111...

NC_000011.9:g.111957664C>T

SDHD RefSeqGene NG_012337.3:g.5094C= NG_012337.3:g.509...

NG_012337.3:g.5094C>A

NG_012337.3:g.509...

NG_012337.3:g.5094C>T

SDHD transcript variant 1 NM_003002.3:c.33C= NM_003002.3:c.33C>A NM_003002.3:c.33C>T
SDHD transcript variant 4 NM_001276506.1:c....

NM_001276506.1:c.33C=

NM_001276506.1:c....

NM_001276506.1:c.33C>A

NM_001276506.1:c....

NM_001276506.1:c.33C>T

SDHD transcript variant 5 NR_077060.1:n.117C= NR_077060.1:n.117C>A NR_077060.1:n.117C>T
SDHD transcript variant 3 NM_001276504.1:c....

NM_001276504.1:c.33C=

NM_001276504.1:c....

NM_001276504.1:c.33C>A

NM_001276504.1:c....

NM_001276504.1:c.33C>T

SDHD transcript variant 2 NM_001276503.1:c....

NM_001276503.1:c.33C=

NM_001276503.1:c....

NM_001276503.1:c.33C>A

NM_001276503.1:c....

NM_001276503.1:c.33C>T

TIMM8B RefSeqGene NG_033145.1:g.4859G= NG_033145.1:g.485...

NG_033145.1:g.4859G>T

NG_033145.1:g.485...

NG_033145.1:g.4859G>A

succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial isoform a precursor NP_002993.1:p.Cys11= NP_002993.1:p.Cys...

NP_002993.1:p.Cys11Ter

NP_002993.1:p.Cys11=
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial isoform d precursor NP_001263435.1:p....

NP_001263435.1:p.Cys11=

NP_001263435.1:p....

NP_001263435.1:p.Cys11Ter

NP_001263435.1:p....

NP_001263435.1:p.Cys11=

succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial isoform c precursor NP_001263433.1:p....

NP_001263433.1:p.Cys11=

NP_001263433.1:p....

NP_001263433.1:p.Cys11Ter

NP_001263433.1:p....

NP_001263433.1:p.Cys11=

succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial isoform b precursor NP_001263432.1:p....

NP_001263432.1:p.Cys11=

NP_001263432.1:p....

NP_001263432.1:p.Cys11Ter

NP_001263432.1:p....

NP_001263432.1:p.Cys11=

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 ClinVar, 2 Frequency, 6 SubSNP submissions
No Submitter Submission ID Date (Build)
1 OMICIA ss244239045 May 28, 2010 (132)
2 OMIM-CURATED-RECORDS ss263193322 Oct 28, 2010 (133)
3 EVA_EXAC ss1690633389 Apr 01, 2015 (144)
4 ILLUMINA ss1959385749 Feb 12, 2016 (147)
5 GNOMAD ss2739389289 Nov 08, 2017 (151)
6 ILLUMINA ss3021376352 Nov 08, 2017 (151)
7 The Exome Aggregation Consortium NC_000011.9 - 111957664 Jul 20, 2018 (151)
8 The Genome Aggregation Database NC_000011.9 - 111957664 Jul 20, 2018 (151)
9 ClinVar RCV000007324.2 Jul 20, 2018 (151)
10 ClinVar RCV000221327.2 Jul 20, 2018 (151)
11 ClinVar RCV000529506.1 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
909448, 8404024, ss1690633389, ss1959385749, ss2739389289, ss3021376352 NC_000011.9:111957663:C= NC_000011.10:112086939:C= (self)
ss244239045, ss263193322 NC_000011.10:112086939:C= NC_000011.10:112086939:C= (self)
ss1959385749, ss3021376352 NC_000011.9:111957663:C>A NC_000011.10:112086939:C>A (self)
RCV000007324.2, RCV000221327.2, RCV000529506.1, ss244239045, ss263193322 NC_000011.10:112086939:C>A NC_000011.10:112086939:C>A (self)
909448, 8404024, ss1690633389, ss2739389289 NC_000011.9:111957663:C>T NC_000011.10:112086939:C>T (self)
Help

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

1 citation for rs104894309
PMID Title Author Year Journal
12000816 Germ-line mutations in nonsyndromic pheochromocytoma. Neumann HP et al. 2002 The New England journal of medicine

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