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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs199422161

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr1:197121989 (GRCh38.p7) 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>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.00001 (2/245024, GnomAD)
T=0.00001 (1/119224, ExAC)
Clinical Significance
Reported in ClinVar
Gene : Consequence
ASPM : 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.p7 chr 1 NC_000001.11:g.197121989C>A
GRCh38.p7 chr 1 NC_000001.11:g.197121989C>T
GRCh37.p13 chr 1 NC_000001.10:g.197091119C>A
GRCh37.p13 chr 1 NC_000001.10:g.197091119C>T
ASPM RefSeqGene NG_015867.1:g.29706G>T
ASPM RefSeqGene NG_015867.1:g.29706G>A
Gene: ASPM, abnormal spindle microtubule assembly (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ASPM transcript variant 1 NM_018136.4:c.379...

NM_018136.4:c.3796G>T

E [GAA] > * [TAA] Coding Sequence Variant
abnormal spindle-like microcephaly-associated protein isoform 1 NP_060606.3:p.Glu...

NP_060606.3:p.Glu1266Ter

E (Glu) > * (Ter) Stop Gained
ASPM transcript variant 1 NM_018136.4:c.379...

NM_018136.4:c.3796G>A

E [GAA] > K [AAA] Coding Sequence Variant
abnormal spindle-like microcephaly-associated protein isoform 1 NP_060606.3:p.Glu...

NP_060606.3:p.Glu1266Lys

E (Glu) > K (Lys) Missense Variant
ASPM transcript variant 2 NM_001206846.1:c....

NM_001206846.1:c.3796G>T

E [GAA] > * [TAA] Coding Sequence Variant
abnormal spindle-like microcephaly-associated protein isoform 2 NP_001193775.1:p....

NP_001193775.1:p.Glu1266Ter

E (Glu) > * (Ter) Stop Gained
ASPM transcript variant 2 NM_001206846.1:c....

NM_001206846.1:c.3796G>A

E [GAA] > K [AAA] Coding Sequence Variant
abnormal spindle-like microcephaly-associated protein isoform 2 NP_001193775.1:p....

NP_001193775.1:p.Glu1266Lys

E (Glu) > K (Lys) Missense 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: A (allele ID: 34434 )
ClinVar Accession Disease Names Clinical Significance
RCV000020772.1 Primary autosomal recessive microcephaly 5 Pathogenic
RCV000216421.1 not provided 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
The Genome Aggregation Database Global Study-wide 245024 C=0.99999 T=0.00000, A=0.00001
The Genome Aggregation Database European Sub 133116 C=0.99998 T=0.00000, A=0.00002
The Genome Aggregation Database Asian Sub 47960 C=1.0000 T=0.0000, A=0.0000
The Genome Aggregation Database American Sub 33424 C=1.0000 T=0.0000, A=0.0000
The Genome Aggregation Database African Sub 15250 C=1.0000 T=0.0000, A=0.0000
The Genome Aggregation Database Ashkenazi Jewish Sub 9832 C=1.000 T=0.000, A=0.000
The Genome Aggregation Database Other Sub 5442 C=1.000 T=0.000, A=0.000
The Exome Aggregation Consortium Global Study-wide 119224 C=0.99999 T=0.00001
The Exome Aggregation Consortium Europe Sub 72058 C=1.0000 T=0.0000
The Exome Aggregation Consortium Asian Sub 24828 C=1.0000 T=0.0000
The Exome Aggregation Consortium American Sub 11300 C=1.0000 T=0.0000
The Exome Aggregation Consortium African Sub 10150 C=1.0000 T=0.0000
The Exome Aggregation Consortium Other Sub 888 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= A T Note
GRCh38.p7 chr 1 NC_000001.11:g.19...

NC_000001.11:g.197121989C=

NC_000001.11:g.19...

NC_000001.11:g.197121989C>A

NC_000001.11:g.19...

NC_000001.11:g.197121989C>T

GRCh37.p13 chr 1 NC_000001.10:g.19...

NC_000001.10:g.197091119C=

NC_000001.10:g.19...

NC_000001.10:g.197091119C>A

NC_000001.10:g.19...

NC_000001.10:g.197091119C>T

ASPM RefSeqGene NG_015867.1:g.297...

NG_015867.1:g.29706G=

NG_015867.1:g.297...

NG_015867.1:g.29706G>T

NG_015867.1:g.297...

NG_015867.1:g.29706G>A

ASPM transcript variant 1 NM_018136.4:c.3796G= NM_018136.4:c.379...

NM_018136.4:c.3796G>T

NM_018136.4:c.379...

NM_018136.4:c.3796G>A

ASPM transcript variant 2 NM_001206846.1:c....

NM_001206846.1:c.3796G=

NM_001206846.1:c....

NM_001206846.1:c.3796G>T

NM_001206846.1:c....

NM_001206846.1:c.3796G>A

abnormal spindle-like microcephaly-associated protein isoform 1 NP_060606.3:p.Glu...

NP_060606.3:p.Glu1266=

NP_060606.3:p.Glu...

NP_060606.3:p.Glu1266Ter

NP_060606.3:p.Glu...

NP_060606.3:p.Glu1266Lys

abnormal spindle-like microcephaly-associated protein isoform 2 NP_001193775.1:p....

NP_001193775.1:p.Glu1266=

NP_001193775.1:p....

NP_001193775.1:p.Glu1266Ter

NP_001193775.1:p....

NP_001193775.1:p.Glu1266Lys

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 Frequency, 4 SubSNP, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 GENEREVIEWS ss475893596 Dec 12, 2011 (136)
2 EVA_EXAC ss1685974022 Apr 01, 2015 (144)
3 HUMAN_LONGEVITY ss2168987522 Dec 20, 2016 (150)
4 GNOMAD ss2732150455 Nov 08, 2017 (151)
5 The Exome Aggregation Consortium NC_000001.10 - 197091119 Jul 19, 2018 (151)
6 The Genome Aggregation Database NC_000001.10 - 197091119 Jul 19, 2018 (151)
7 ClinVar RCV000020772.1 Jul 19, 2018 (151)
8 ClinVar RCV000216421.1 Jul 19, 2018 (151)
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
5204984, 1165190, ss1685974022, ss2732150455 NC_000001.10:197091118:C= NC_000001.11:197121988:C= (self)
ss475893596, ss2168987522 NC_000001.11:197121988:C= NC_000001.11:197121988:C= (self)
1165190, ss2732150455 NC_000001.10:197091118:C>A NC_000001.11:197121988:C>A (self)
RCV000020772.1, RCV000216421.1, ss475893596, ss2168987522 NC_000001.11:197121988:C>A NC_000001.11:197121988:C>A (self)
5204984, 1165190, ss1685974022, ss2732150455 NC_000001.10:197091118:C>T NC_000001.11:197121988: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 rs199422161
PMID Title Author Year Journal
20301772 Primary Autosomal Recessive Microcephalies and Seckel Syndrome Spectrum Disorders Verloes A et al. 1993 GeneReviews®

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: 0.1.4.post833+d3ba21e