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dbSNP Short Genetic Variations

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 Aliases 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.

rs753555873

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr12:120557443 (GRCh38.p12) 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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.00000 (1/251298, GnomAD_exome)
C=0.00001 (1/121394, ExAC)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RNF10 : Synonymous Variant
Publications
0 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.p12 chr 12 NC_000012.12:g.120557443T>C
GRCh37.p13 chr 12 NC_000012.11:g.120995246T>C
Gene: RNF10, ring finger protein 10 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
RNF10 transcript variant 1 NM_014868.5:c.807T>C S [TCT] > S [TCC] Coding Sequence Variant
RING finger protein 10 isoform 1 NP_055683.3:p.Ser269= S (Ser) > S (Ser) Synonymous Variant
RNF10 transcript variant 2 NM_001330474.2:c.807T>C S [TCT] > S [TCC] Coding Sequence Variant
RING finger protein 10 isoform 2 NP_001317403.1:p.Ser269= S (Ser) > S (Ser) Synonymous Variant
RNF10 transcript variant X1 XM_005254013.2:c.657T>C S [TCT] > S [TCC] Coding Sequence Variant
RING finger protein 10 isoform X1 XP_005254070.1:p.Ser219= S (Ser) > S (Ser) Synonymous Variant
RNF10 transcript variant X2 XM_017020282.1:c.657T>C S [TCT] > S [TCC] Coding Sequence Variant
RING finger protein 10 isoform X2 XP_016875771.1:p.Ser219= S (Ser) > S (Ser) Synonymous Variant
RNF10 transcript variant X5 XM_017020283.2:c.807T>C S [TCT] > S [TCC] Coding Sequence Variant
RING finger protein 10 isoform X3 XP_016875772.1:p.Ser269= S (Ser) > S (Ser) Synonymous Variant
RNF10 transcript variant X12 XR_001748939.1:n.1367T>C N/A Non Coding Transcript Variant
RNF10 transcript variant X3 XR_944849.3:n.1266T>C N/A Non Coding Transcript Variant
RNF10 transcript variant X4 XR_001748933.2:n.1266T>C N/A Non Coding Transcript Variant
RNF10 transcript variant X6 XR_001748934.2:n.1266T>C N/A Non Coding Transcript Variant
RNF10 transcript variant X7 XR_001748935.2:n.1266T>C N/A Non Coding Transcript Variant
RNF10 transcript variant X8 XR_243026.4:n.1266T>C N/A Non Coding Transcript Variant
RNF10 transcript variant X9 XR_001748936.2:n.1266T>C N/A Non Coding Transcript Variant
RNF10 transcript variant X10 XR_001748937.2:n.1266T>C N/A Non Coding Transcript Variant
RNF10 transcript variant X11 XR_001748938.2:n.1266T>C 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.

Not Reported in ClinVar
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
gnomAD - Exomes Global Study-wide 251298 T=1.00000 C=0.00000
gnomAD - Exomes European Sub 135262 T=1.00000 C=0.00000
gnomAD - Exomes Asian Sub 49008 T=1.0000 C=0.0000
gnomAD - Exomes American Sub 34576 T=1.0000 C=0.0000
gnomAD - Exomes African Sub 16256 T=1.0000 C=0.0000
gnomAD - Exomes Ashkenazi Jewish Sub 10070 T=1.0000 C=0.0000
gnomAD - Exomes Other Sub 6126 T=1.000 C=0.000
ExAC Global Study-wide 121394 T=0.99999 C=0.00001
ExAC Europe Sub 73338 T=1.0000 C=0.0000
ExAC Asian Sub 25164 T=1.0000 C=0.0000
ExAC American Sub 11578 T=1.0000 C=0.0000
ExAC African Sub 10406 T=1.0000 C=0.0000
ExAC Other Sub 908 T=1.00 C=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 T= C Note
GRCh38.p12 chr 12 NC_000012.12:g.120557443= NC_000012.12:g.12055744...

NC_000012.12:g.120557443T>C

GRCh37.p13 chr 12 NC_000012.11:g.120995246= NC_000012.11:g.12099524...

NC_000012.11:g.120995246T>C

RNF10 transcript variant 1 NM_014868.5:c.807= NM_014868.5:c.807T>C
RNF10 transcript variant 1 NM_014868.4:c.807= NM_014868.4:c.807T>C
RNF10 transcript variant X8 XR_243026.4:n.1266= XR_243026.4:n.1266T>C
RNF10 transcript variant X6 XR_243026.1:n.928= XR_243026.1:n.928T>C
RNF10 transcript variant X3 XR_944849.3:n.1266= XR_944849.3:n.1266T>C
RNF10 transcript variant X1 XM_005254013.2:c.657= XM_005254013.2:c.657T>C
RNF10 transcript variant X2 XM_005254013.1:c.657= XM_005254013.1:c.657T>C
RNF10 transcript variant X7 XR_001748935.2:n.1266= XR_001748935.2:n.1266T>C
RNF10 transcript variant X4 XR_001748933.2:n.1266= XR_001748933.2:n.1266T>C
RNF10 transcript variant X10 XR_001748937.2:n.1266= XR_001748937.2:n.1266T>C
RNF10 transcript variant X11 XR_001748938.2:n.1266= XR_001748938.2:n.1266T>C
RNF10 transcript variant X9 XR_001748936.2:n.1266= XR_001748936.2:n.1266T>C
RNF10 transcript variant X6 XR_001748934.2:n.1266= XR_001748934.2:n.1266T>C
RNF10 transcript variant X5 XM_017020283.2:c.807= XM_017020283.2:c.807T>C
RNF10 transcript variant X2 XM_017020282.1:c.657= XM_017020282.1:c.657T>C
RNF10 transcript variant 2 NM_001330474.1:c.807= NM_001330474.1:c.807T>C
RNF10 transcript variant 2 NM_001330474.2:c.807= NM_001330474.2:c.807T>C
RNF10 transcript variant X12 XR_001748939.1:n.1367= XR_001748939.1:n.1367T>C
RING finger protein 10 isoform 1 NP_055683.3:p.Ser269= NP_055683.3:p.Ser269=
RING finger protein 10 isoform X1 XP_005254070.1:p.Ser219= XP_005254070.1:p.Ser219=
RING finger protein 10 isoform X3 XP_016875772.1:p.Ser269= XP_016875772.1:p.Ser269=
RING finger protein 10 isoform X2 XP_016875771.1:p.Ser219= XP_016875771.1:p.Ser219=
RING finger protein 10 isoform 2 NP_001317403.1:p.Ser269= NP_001317403.1:p.Ser269=
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#.

2 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1691147414 Apr 01, 2015 (144)
2 GNOMAD ss2740194587 Nov 08, 2017 (151)
3 ExAC NC_000012.11 - 120995246 Oct 12, 2018 (152)
4 gnomAD - Exomes NC_000012.11 - 120995246 Jul 13, 2019 (153)
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
1464545, 9433341, ss1691147414, ss2740194587 NC_000012.11:120995245:T:C NC_000012.12:120557442:T:C (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 rs753555873

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.post308+0fe9b3b