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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.

rs1007345781

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr3:180616604-180616606 (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
delGT
Variation Type
Indel Insertion and Deletion
Frequency
delGT=0.00000 (1/226612, GnomAD)
delGT=0.00006 (8/125568, TOPMED)
delGT=0.0001 (2/30934, GnomAD)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CCDC39 : Frameshift
TTC14 : Intron 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 3 NC_000003.12:g.180616605_180616606delGT
GRCh37.p13 chr 3 NC_000003.11:g.180334393_180334394delGT
CCDC39 RefSeqGene NG_029581.1:g.67891_67892delCA
Gene: TTC14, tetratricopeptide repeat domain 14 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TTC14 transcript variant 3 NM_001288582.1:c. N/A Intron Variant
TTC14 transcript variant 2 NM_001042601.2:c. N/A Genic Downstream Transcript Variant
TTC14 transcript variant 1 NM_133462.3:c. N/A Genic Downstream Transcript Variant
TTC14 transcript variant X1 XM_017005739.2:c. N/A Genic Downstream Transcript Variant
TTC14 transcript variant X5 XM_017005740.2:c. N/A Genic Downstream Transcript Variant
TTC14 transcript variant X2 XM_024453361.1:c. N/A Genic Downstream Transcript Variant
TTC14 transcript variant X3 XR_001740029.2:n. N/A Genic Downstream Transcript Variant
TTC14 transcript variant X4 XR_001740030.2:n. N/A Genic Downstream Transcript Variant
TTC14 transcript variant X6 XR_427362.4:n. N/A Genic Downstream Transcript Variant
Gene: CCDC39, coiled-coil domain containing 39 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CCDC39 transcript NM_181426.1:c.2497_2498...

NM_181426.1:c.2497_2498delCA

Q [CA] > V [G] Coding Sequence Variant
coiled-coil domain-containing protein 39 NP_852091.1:p.Gln833fs Q (Gln) > V (Val) Frameshift
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: delGT (allele ID: 452208 )
ClinVar Accession Disease Names Clinical Significance
RCV000529219.2 Ciliary dyskinesia 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
gnomAD - Exomes Global Study-wide 226612 -

No frequency provided

delGT=0.00000
gnomAD - Exomes European Sub 123262 -

No frequency provided

delGT=0.00000
gnomAD - Exomes Asian Sub 44064 -

No frequency provided

delGT=0.0000
gnomAD - Exomes American Sub 31372 -

No frequency provided

delGT=0.0000
gnomAD - Exomes African Sub 13708 -

No frequency provided

delGT=0.0001
gnomAD - Exomes Ashkenazi Jewish Sub 9152 -

No frequency provided

delGT=0.000
gnomAD - Exomes Other Sub 5054 -

No frequency provided

delGT=0.000
TopMed Global Study-wide 125568 -

No frequency provided

delGT=0.00006
gnomAD - Genomes Global Study-wide 30934 -

No frequency provided

delGT=0.0001
gnomAD - Genomes European Sub 18472 -

No frequency provided

delGT=0.0000
gnomAD - Genomes African Sub 8726 -

No frequency provided

delGT=0.000
gnomAD - Genomes East Asian Sub 1618 -

No frequency provided

delGT=0.000
gnomAD - Genomes Other Sub 978 -

No frequency provided

delGT=0.00
gnomAD - Genomes American Sub 838 -

No frequency provided

delGT=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 302 -

No frequency provided

delGT=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 TGT= delGT Note
GRCh38.p12 chr 3 NC_000003.12:g.18061660...

NC_000003.12:g.180616604_180616606TGT=

NC_000003.12:g.18061660...

NC_000003.12:g.180616605_180616606delGT

GRCh37.p13 chr 3 NC_000003.11:g.18033439...

NC_000003.11:g.180334392_180334394TGT=

NC_000003.11:g.18033439...

NC_000003.11:g.180334393_180334394delGT

CCDC39 RefSeqGene NG_029581.1:g.67890_678...

NG_029581.1:g.67890_67892ACA=

NG_029581.1:g.67891_678...

NG_029581.1:g.67891_67892delCA

CCDC39 transcript NM_181426.1:c.2496_2498...

NM_181426.1:c.2496_2498ACA=

NM_181426.1:c.2497_2498...

NM_181426.1:c.2497_2498delCA

coiled-coil domain-containing protein 39 NP_852091.1:p.Lys832_Gl...

NP_852091.1:p.Lys832_Gln833=

NP_852091.1:p.Gln833fs
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#.

5 SubSNP, 3 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 TOPMED ss2426087388 Dec 20, 2016 (150)
2 GNOMAD ss2734217043 Nov 08, 2017 (151)
3 GNOMAD ss2747144321 Nov 08, 2017 (151)
4 GNOMAD ss2803048131 Nov 08, 2017 (151)
5 TOPMED ss3414514807 Nov 08, 2017 (151)
6 gnomAD - Genomes NC_000003.11 - 180334392 Oct 12, 2018 (152)
7 gnomAD - Exomes NC_000003.11 - 180334392 Oct 12, 2018 (152)
8 TopMed NC_000003.12 - 180616604 Oct 12, 2018 (152)
9 ClinVar RCV000529219.2 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
143675885, 2636299, ss2426087388, ss2734217043, ss2747144321, ss2803048131 NC_000003.11:180334391:TG: NC_000003.12:180616603:TGT:T (self)
RCV000529219.2, 270618573, ss3414514807 NC_000003.12:180616603:TG: NC_000003.12:180616603:TGT:T (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 rs1007345781

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.post104+4a6ee9c