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dbSNP Short Genetic Variations

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.

rs121912997

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr6:7579989 (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
C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.00001 (1/125568, TOPMED)
T=0.0000 (0/78688, PAGE_STUDY)
Clinical Significance
Reported in ClinVar
Gene : Consequence
DSP : Stop Gained
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.p12 chr 6 NC_000006.12:g.7579989C>G
GRCh38.p12 chr 6 NC_000006.12:g.7579989C>T
GRCh37.p13 chr 6 NC_000006.11:g.7580222C>G
GRCh37.p13 chr 6 NC_000006.11:g.7580222C>T
DSP RefSeqGene (LRG_423) NG_008803.1:g.43353C>G
DSP RefSeqGene (LRG_423) NG_008803.1:g.43353C>T
Gene: DSP, desmoplakin (plus strand)
Molecule type Change Amino acid[Codon] SO Term
DSP transcript variant 2 NM_001008844.3:c. N/A Intron Variant
DSP transcript variant 1 NM_004415.4:c.3799C>G R [CGA] > G [GGA] Coding Sequence Variant
desmoplakin isoform I NP_004406.2:p.Arg1267Gly R (Arg) > G (Gly) Missense Variant
DSP transcript variant 1 NM_004415.4:c.3799C>T R [CGA] > * [TGA] Coding Sequence Variant
desmoplakin isoform I NP_004406.2:p.Arg1267Ter R (Arg) > * (Ter) Stop Gained
DSP transcript variant 3 NM_001319034.2:c.3799C>G R [CGA] > G [GGA] Coding Sequence Variant
desmoplakin isoform Ia NP_001305963.1:p.Arg126...

NP_001305963.1:p.Arg1267Gly

R (Arg) > G (Gly) Missense Variant
DSP transcript variant 3 NM_001319034.2:c.3799C>T R [CGA] > * [TGA] Coding Sequence Variant
desmoplakin isoform Ia NP_001305963.1:p.Arg126...

NP_001305963.1:p.Arg1267Ter

R (Arg) > * (Ter) Stop Gained
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: 31884 )
ClinVar Accession Disease Names Clinical Significance
RCV000018339.24 Dilated cardiomyopathy with woolly hair and keratoderma Pathogenic
RCV000157195.1 Long QT syndrome,Primary dilated cardiomyopathy Likely-Pathogenic
RCV000598733.1 not provided Likely-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
TopMed Global Study-wide 125568 C=0.99999 G=0.00001
The PAGE Study Global Study-wide 78688 C=1.0000 T=0.0000
The PAGE Study AfricanAmerican Sub 32508 C=1.0000 T=0.0000
The PAGE Study Mexican Sub 10810 C=1.0000 T=0.0000
The PAGE Study Asian Sub 8318 C=1.000 T=0.000
The PAGE Study PuertoRican Sub 7918 C=1.000 T=0.000
The PAGE Study NativeHawaiian Sub 4530 C=1.000 T=0.000
The PAGE Study Cuban Sub 4228 C=1.000 T=0.000
The PAGE Study Dominican Sub 3828 C=1.000 T=0.000
The PAGE Study CentralAmerican Sub 2450 C=1.000 T=0.000
The PAGE Study SouthAmerican Sub 1982 C=1.000 T=0.000
The PAGE Study NativeAmerican Sub 1260 C=1.000 T=0.000
The PAGE Study SouthAsian Sub 856 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= G T Note
GRCh38.p12 chr 6 NC_000006.12:g.75...

NC_000006.12:g.7579989=

NC_000006.12:g.75...

NC_000006.12:g.7579989C>G

NC_000006.12:g.75...

NC_000006.12:g.7579989C>T

GRCh37.p13 chr 6 NC_000006.11:g.75...

NC_000006.11:g.7580222=

NC_000006.11:g.75...

NC_000006.11:g.7580222C>G

NC_000006.11:g.75...

NC_000006.11:g.7580222C>T

DSP RefSeqGene (LRG_423) NG_008803.1:g.43353= NG_008803.1:g.433...

NG_008803.1:g.43353C>G

NG_008803.1:g.433...

NG_008803.1:g.43353C>T

DSP transcript variant 1 NM_004415.4:c.3799= NM_004415.4:c.379...

NM_004415.4:c.3799C>G

NM_004415.4:c.379...

NM_004415.4:c.3799C>T

DSP transcript variant 1 NM_004415.3:c.3799= NM_004415.3:c.379...

NM_004415.3:c.3799C>G

NM_004415.3:c.379...

NM_004415.3:c.3799C>T

DSP transcript variant 1 NM_004415.2:c.3799= NM_004415.2:c.379...

NM_004415.2:c.3799C>G

NM_004415.2:c.379...

NM_004415.2:c.3799C>T

DSP transcript variant 3 NM_001319034.1:c....

NM_001319034.1:c.3799=

NM_001319034.1:c....

NM_001319034.1:c.3799C>G

NM_001319034.1:c....

NM_001319034.1:c.3799C>T

DSP transcript variant 3 NM_001319034.2:c....

NM_001319034.2:c.3799=

NM_001319034.2:c....

NM_001319034.2:c.3799C>G

NM_001319034.2:c....

NM_001319034.2:c.3799C>T

desmoplakin isoform I NP_004406.2:p.Arg...

NP_004406.2:p.Arg1267=

NP_004406.2:p.Arg...

NP_004406.2:p.Arg1267Gly

NP_004406.2:p.Arg...

NP_004406.2:p.Arg1267Ter

desmoplakin isoform Ia NP_001305963.1:p....

NP_001305963.1:p.Arg1267=

NP_001305963.1:p....

NP_001305963.1:p.Arg1267Gly

NP_001305963.1:p....

NP_001305963.1:p.Arg1267Ter

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#.

8 SubSNP, 2 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss275514414 Nov 22, 2010 (133)
2 ILLUMINA ss1958860669 Feb 12, 2016 (147)
3 AFFY ss2985980748 Nov 08, 2017 (151)
4 ILLUMINA ss3022572270 Nov 08, 2017 (151)
5 TOPMED ss3489445001 Nov 08, 2017 (151)
6 ILLUMINA ss3653080226 Oct 12, 2018 (152)
7 ILLUMINA ss3726308142 Jul 13, 2019 (153)
8 PAGE_CC ss3771260707 Jul 13, 2019 (153)
9 The PAGE Study NC_000006.12 - 7579989 Jul 13, 2019 (153)
10 TopMed NC_000006.12 - 7579989 Oct 12, 2018 (152)
11 ClinVar RCV000018339.24 Oct 12, 2018 (152)
12 ClinVar RCV000157195.1 Oct 12, 2018 (152)
13 ClinVar RCV000598733.1 Oct 12, 2018 (152)
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
331502983, ss3489445001 NC_000006.12:7579988:C:G NC_000006.12:7579988:C:G (self)
ss1958860669, ss2985980748, ss3022572270, ss3653080226 NC_000006.11:7580221:C:T NC_000006.12:7579988:C:T (self)
RCV000018339.24, RCV000157195.1, RCV000598733.1, 482176, ss275514414, ss3726308142, ss3771260707 NC_000006.12:7579988:C:T NC_000006.12:7579988: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 rs121912997
PMID Title Author Year Journal
16467215 Loss of desmoplakin isoform I causes early onset cardiomyopathy and heart failure in a Naxos-like syndrome. Uzumcu A et al. 2006 Journal of medical genetics

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.post246+3cda961