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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 HGVS 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.

rs778417218

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr17:50186312 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000060 (15/251156, GnomAD_exome)
T=0.000104 (13/125568, TOPMED)
T=0.000074 (9/121398, ExAC) (+ 4 more)
T=0.00006 (2/31406, GnomAD)
T=0.00009 (1/11176, dbGaP Population Frequency Project)
T=0.0003 (1/3854, ALSPAC)
T=0.0000 (0/3708, TWINSUK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
COL1A1 : 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 17 NC_000017.11:g.50186312C>T
GRCh37.p13 chr 17 NC_000017.10:g.48263673C>T
COL1A1 RefSeqGene (LRG_1) NG_007400.1:g.20328G>A
Gene: COL1A1, collagen type I alpha 1 chain (minus strand)
Molecule type Change Amino acid[Codon] SO Term
COL1A1 transcript NM_000088.4:c.4005+5G>A N/A Intron Variant
COL1A1 transcript variant X2 XM_005257058.4:c.3735+5G>A N/A Intron Variant
COL1A1 transcript variant X3 XM_005257059.4:c.3087+5G>A N/A Intron Variant
COL1A1 transcript variant X1 XM_011524341.1:c.3807+5G>A N/A Intron 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: 438049 )
ClinVar Accession Disease Names Clinical Significance
RCV000513599.2 not provided Uncertain-Significance
RCV000631475.1 Osteogenesis imperfecta type I Uncertain-Significance
RCV001001319.1 not specified Uncertain-Significance
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").

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Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 251156 C=0.999940 T=0.000060
gnomAD - Exomes European Sub 135082 C=0.999896 T=0.000104
gnomAD - Exomes Asian Sub 49008 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 34592 C=0.99997 T=0.00003
gnomAD - Exomes African Sub 16256 C=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10078 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6140 C=1.0000 T=0.0000
TopMed Global Study-wide 125568 C=0.999896 T=0.000104
ExAC Global Study-wide 121398 C=0.999926 T=0.000074
ExAC Europe Sub 73348 C=0.99988 T=0.00012
ExAC Asian Sub 25162 C=1.00000 T=0.00000
ExAC American Sub 11576 C=1.00000 T=0.00000
ExAC African Sub 10406 C=1.00000 T=0.00000
ExAC Other Sub 906 C=1.000 T=0.000
gnomAD - Genomes Global Study-wide 31406 C=0.99994 T=0.00006
gnomAD - Genomes European Sub 18904 C=0.99989 T=0.00011
gnomAD - Genomes African Sub 8716 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 1560 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 1088 C=1.0000 T=0.0000
gnomAD - Genomes American Sub 848 C=1.000 T=0.000
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=1.000 T=0.000
ALFA Total Global 11176 C=0.99991 T=0.00009
ALFA European Sub 8134 C=0.9999 T=0.0001
ALFA Other Sub 2302 C=1.0000 T=0.0000
ALFA African Sub 676 C=1.000 T=0.000
ALFA Asian Sub 60 C=1.00 T=0.00
ALFA South Asian Sub 4 C=1.0 T=0.0
ALFA Latin American 1 Sub 0 C=0 T=0
ALFA Latin American 2 Sub 0 C=0 T=0
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9997 T=0.0003
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=1.0000 T=0.0000
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= T
GRCh38.p12 chr 17 NC_000017.11:g.50186312= NC_000017.11:g.50186312C>T
GRCh37.p13 chr 17 NC_000017.10:g.48263673= NC_000017.10:g.48263673C>T
COL1A1 RefSeqGene (LRG_1) NG_007400.1:g.20328= NG_007400.1:g.20328G>A
COL1A1 transcript NM_000088.3:c.4005+5= NM_000088.3:c.4005+5G>A
COL1A1 transcript NM_000088.4:c.4005+5= NM_000088.4:c.4005+5G>A
COL1A1 transcript variant X1 XM_005257058.1:c.3735+5= XM_005257058.1:c.3735+5G>A
COL1A1 transcript variant X2 XM_005257058.4:c.3735+5= XM_005257058.4:c.3735+5G>A
COL1A1 transcript variant X2 XM_005257059.1:c.3087+5= XM_005257059.1:c.3087+5G>A
COL1A1 transcript variant X3 XM_005257059.4:c.3087+5= XM_005257059.4:c.3087+5G>A
COL1A1 transcript variant X1 XM_011524341.1:c.3807+5= XM_011524341.1:c.3807+5G>A
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#.

10 SubSNP, 7 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EVA_UK10K_ALSPAC ss1635745311 Apr 01, 2015 (144)
2 EVA_UK10K_TWINSUK ss1678739344 Apr 01, 2015 (144)
3 EVA_EXAC ss1692853076 Apr 01, 2015 (144)
4 HUMAN_LONGEVITY ss2217219365 Dec 20, 2016 (150)
5 TOPMED ss2382374852 Dec 20, 2016 (150)
6 GNOMAD ss2742835783 Nov 08, 2017 (151)
7 GNOMAD ss2749810145 Nov 08, 2017 (151)
8 GNOMAD ss2950466907 Nov 08, 2017 (151)
9 TOPMED ss3264201822 Nov 08, 2017 (151)
10 EVA_DECODE ss3700567970 Jul 13, 2019 (153)
11 The Avon Longitudinal Study of Parents and Children NC_000017.10 - 48263673 Oct 12, 2018 (152)
12 ExAC NC_000017.10 - 48263673 Oct 12, 2018 (152)
13 gnomAD - Genomes NC_000017.10 - 48263673 Jul 13, 2019 (153)
14 gnomAD - Exomes NC_000017.10 - 48263673 Jul 13, 2019 (153)
15 TopMed NC_000017.11 - 50186312 Oct 12, 2018 (152)
16 UK 10K study - Twins NC_000017.10 - 48263673 Oct 12, 2018 (152)
17 dbGaP Population Frequency Project NC_000017.11 - 50186312 Apr 27, 2020 (154)
18 ClinVar RCV000513599.2 Apr 27, 2020 (154)
19 ClinVar RCV000631475.1 Oct 12, 2018 (152)
20 ClinVar RCV001001319.1 Apr 27, 2020 (154)
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
39952771, 3302056, 196763144, 12139440, 39952771, ss1635745311, ss1678739344, ss1692853076, ss2382374852, ss2742835783, ss2749810145, ss2950466907 NC_000017.10:48263672:C:T NC_000017.11:50186311:C:T (self)
RCV000513599.2, RCV000631475.1, RCV001001319.1, 158022890, 873565555, ss2217219365, ss3264201822, ss3700567970 NC_000017.11:50186311:C:T NC_000017.11:50186311: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.

No publications for rs778417218

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

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.post557+f76c771