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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.

rs34083643

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr17:17793788 (GRCh38.p13) 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
delG
Variation Type
Deletion
Frequency
delG=0.237026 (42962/181254, GnomAD_exome)
delG=0.357409 (47920/134076, GnomAD)
delG=0.412184 (43328/105118, ExAC) (+ 3 more)
G=0.19388 (3249/16758, 8.3KJPN)
delG=0.00089 (10/11272, ALFA)
delG=0.235 (141/600, NorthernSweden)
Clinical Significance
Reported in ClinVar
Gene : Consequence
RAI1 : Frameshift Variant
Publications
0 citations
Genomic View
See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 8189 G=0.9988 =0.0012
European Sub 5453 G=0.9991 =0.0009
African Sub 1850 G=0.9989 =0.0011
African Others Sub 69 G=1.00 =0.00
African American Sub 1781 G=0.9989 =0.0011
Asian Sub 47 G=1.00 =0.00
East Asian Sub 36 G=1.00 =0.00
Other Asian Sub 11 G=1.00 =0.00
Latin American 1 Sub 99 G=1.00 =0.00
Latin American 2 Sub 366 G=1.000 =0.000
South Asian Sub 47 G=1.00 =0.00
Other Sub 327 G=0.991 =0.009


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 181254 G=0.762974 delG=0.237026
gnomAD - Exomes European Sub 102196 G=0.861589 delG=0.138411
gnomAD - Exomes Asian Sub 32828 G=0.50006 delG=0.49994
gnomAD - Exomes American Sub 23600 G=0.64360 delG=0.35640
gnomAD - Exomes African Sub 10992 G=0.83142 delG=0.16858
gnomAD - Exomes Ashkenazi Jewish Sub 7328 G=0.8216 delG=0.1784
gnomAD - Exomes Other Sub 4310 G=0.8065 delG=0.1935
gnomAD - Genomes Global Study-wide 134076 G=0.642591 delG=0.357409
gnomAD - Genomes European Sub 71770 G=0.68070 delG=0.31930
gnomAD - Genomes African Sub 41166 G=0.65165 delG=0.34835
gnomAD - Genomes American Sub 13070 G=0.52402 delG=0.47598
gnomAD - Genomes East Asian Sub 3078 G=0.1481 delG=0.8519
gnomAD - Genomes Ashkenazi Jewish Sub 2972 G=0.6487 delG=0.3513
gnomAD - Genomes Other Sub 2020 G=0.6153 delG=0.3847
ExAC Global Study-wide 105118 G=0.587816 delG=0.412184
ExAC Europe Sub 61524 G=0.69431 delG=0.30569
ExAC Asian Sub 24080 G=0.36034 delG=0.63966
ExAC American Sub 10966 G=0.44611 delG=0.55389
ExAC African Sub 7786 G=0.6517 delG=0.3483
ExAC Other Sub 762 G=0.564 delG=0.436
8.3KJPN JAPANESE Study-wide 16758 G=0.19388 delG=0.80612
Northern Sweden ACPOP Study-wide 600 G=0.765 delG=0.235
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.p13 chr 17 NC_000017.11:g.17793788del
GRCh37.p13 chr 17 NC_000017.10:g.17697102del
RAI1 RefSeqGene NG_007101.2:g.117316del
Gene: RAI1, retinoic acid induced 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
RAI1 transcript NM_030665.4:c.840del Q [CAG] > H [CA] Coding Sequence Variant
retinoic acid-induced protein 1 NP_109590.3:p.Gln280fs Q (Gln) > H (His) Frameshift Variant
RAI1 transcript variant X1 XM_017024025.1:c.840del Q [CAG] > H [CA] Coding Sequence Variant
retinoic acid-induced protein 1 isoform X1 XP_016879514.1:p.Gln280fs Q (Gln) > H (His) Frameshift Variant
RAI1 transcript variant X2 XM_017024026.1:c.840del Q [CAG] > H [CA] Coding Sequence Variant
retinoic acid-induced protein 1 isoform X1 XP_016879515.1:p.Gln280fs Q (Gln) > H (His) Frameshift Variant
RAI1 transcript variant X3 XM_017024027.1:c.840del Q [CAG] > H [CA] Coding Sequence Variant
retinoic acid-induced protein 1 isoform X1 XP_016879516.1:p.Gln280fs Q (Gln) > H (His) Frameshift Variant
RAI1 transcript variant X4 XM_017024028.2:c.840del Q [CAG] > H [CA] Coding Sequence Variant
retinoic acid-induced protein 1 isoform X1 XP_016879517.1:p.Gln280fs Q (Gln) > H (His) Frameshift 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: delG (allele ID: 580293 )
ClinVar Accession Disease Names Clinical Significance
RCV000715201.1 History of neurodevelopmental disorder Benign
RCV000989763.1 Smith-Magenis syndrome Benign
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 G= delG
GRCh38.p13 chr 17 NC_000017.11:g.17793788= NC_000017.11:g.17793788del
GRCh37.p13 chr 17 NC_000017.10:g.17697102= NC_000017.10:g.17697102del
RAI1 RefSeqGene NG_007101.2:g.117316= NG_007101.2:g.117316del
RAI1 transcript NM_030665.4:c.840= NM_030665.4:c.840del
RAI1 transcript NM_030665.3:c.840= NM_030665.3:c.840del
RAI1 transcript variant X4 XM_017024028.2:c.840= XM_017024028.2:c.840del
RAI1 transcript variant X2 XM_017024026.1:c.840= XM_017024026.1:c.840del
RAI1 transcript variant X3 XM_017024027.1:c.840= XM_017024027.1:c.840del
RAI1 transcript variant X1 XM_017024025.1:c.840= XM_017024025.1:c.840del
RAI1 transcript variant 1 NM_017574.1:c.840= NM_017574.1:c.840del
RAI1 transcript variant 2 NM_152256.1:c.840= NM_152256.1:c.840del
retinoic acid-induced protein 1 NP_109590.3:p.Gln280= NP_109590.3:p.Gln280fs
retinoic acid-induced protein 1 isoform X1 XP_016879517.1:p.Gln280= XP_016879517.1:p.Gln280fs
retinoic acid-induced protein 1 isoform X1 XP_016879515.1:p.Gln280= XP_016879515.1:p.Gln280fs
retinoic acid-induced protein 1 isoform X1 XP_016879516.1:p.Gln280= XP_016879516.1:p.Gln280fs
retinoic acid-induced protein 1 isoform X1 XP_016879514.1:p.Gln280= XP_016879514.1:p.Gln280fs
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#.

11 SubSNP, 6 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 ABI ss40836052 Mar 13, 2006 (126)
2 EVA_EXAC ss1712133728 Apr 01, 2015 (144)
3 JJLAB ss2031329455 Sep 14, 2016 (149)
4 MCHAISSO ss3063862278 Nov 08, 2017 (151)
5 MCHAISSO ss3064704805 Nov 08, 2017 (151)
6 MCHAISSO ss3065642694 Nov 08, 2017 (151)
7 ACPOP ss3741921333 Jul 13, 2019 (153)
8 EVA ss3834808661 Apr 27, 2020 (154)
9 TOMMO_GENOMICS ss5221742997 Apr 26, 2021 (155)
10 EVA ss5236940509 Apr 26, 2021 (155)
11 EVA ss5237238015 Apr 26, 2021 (155)
12 ExAC NC_000017.10 - 17697102 Oct 12, 2018 (152)
13 gnomAD - Genomes NC_000017.11 - 17793788 Apr 26, 2021 (155)
14 gnomAD - Exomes NC_000017.10 - 17697102 Jul 13, 2019 (153)
15 Northern Sweden NC_000017.10 - 17697102 Jul 13, 2019 (153)
16 8.3KJPN NC_000017.10 - 17697102 Apr 26, 2021 (155)
17 ALFA NC_000017.11 - 17793788 Apr 26, 2021 (155)
18 ClinVar RCV000715201.1 Jul 13, 2019 (153)
19 ClinVar RCV000989763.1 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
3073146, 11804971, 15206198, 79712304, ss1712133728, ss2031329455, ss3741921333, ss3834808661, ss5221742997 NC_000017.10:17697101:G: NC_000017.11:17793787:G: (self)
RCV000715201.1, RCV000989763.1, 502963880, 10870480724, ss3063862278, ss3064704805, ss3065642694, ss5236940509, ss5237238015 NC_000017.11:17793787:G: NC_000017.11:17793787:G: (self)
ss40836052 NT_010718.16:17300475:G: NC_000017.11:17793787:G: (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 rs34083643

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.post629+eb05767