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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.

rs398124167

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr2:151706880 (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
T=0.00002 (4/216496, GnomAD)
T=0.00002 (3/125568, TOPMED)
A=0.0000 (1/46508, ExAC)
Clinical Significance
Reported in ClinVar
Gene : Consequence
NEB : Splice Donor Variant
Publications
2 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.p7 chr 2 NC_000002.12:g.151706880C>A
GRCh38.p7 chr 2 NC_000002.12:g.151706880C>T
GRCh37.p13 chr 2 NC_000002.11:g.152563394C>A
GRCh37.p13 chr 2 NC_000002.11:g.152563394C>T
NEB RefSeqGene (LRG_202) NG_009382.2:g.32608G>T
NEB RefSeqGene (LRG_202) NG_009382.2:g.32608G>A
Gene: NEB, nebulin (minus strand)
Molecule type Change Amino acid[Codon] SO Term
NEB transcript variant 1 NM_001164507.1:c. N/A Splice Donor Variant
NEB transcript variant 2 NM_001164508.1:c. N/A Splice Donor Variant
NEB transcript variant 4 NM_001271208.1:c. N/A Splice Donor Variant
NEB transcript variant 3 NM_004543.4:c. N/A Splice Donor Variant
NEB transcript variant X1 XM_005246590.2:c. N/A Splice Donor Variant
NEB transcript variant X2 XM_005246591.2:c. N/A Splice Donor Variant
NEB transcript variant X5 XM_005246592.2:c. N/A Splice Donor Variant
NEB transcript variant X3 XM_005246593.2:c. N/A Splice Donor Variant
NEB transcript variant X4 XM_005246594.2:c. N/A Splice Donor Variant
NEB transcript variant X7 XM_005246596.2:c. N/A Splice Donor Variant
NEB transcript variant X9 XM_005246597.2:c. N/A Splice Donor Variant
NEB transcript variant X10 XM_005246598.2:c. N/A Splice Donor Variant
NEB transcript variant X11 XM_005246599.2:c. N/A Splice Donor Variant
NEB transcript variant X12 XM_005246600.2:c. N/A Splice Donor Variant
NEB transcript variant X12 XM_005246601.2:c. N/A Splice Donor Variant
NEB transcript variant X13 XM_005246602.2:c. N/A Splice Donor Variant
NEB transcript variant X14 XM_005246603.2:c. N/A Splice Donor Variant
NEB transcript variant X15 XM_005246604.2:c. N/A Splice Donor Variant
NEB transcript variant X18 XM_005246606.2:c. N/A Splice Donor Variant
NEB transcript variant X22 XM_005246608.2:c. N/A Splice Donor Variant
NEB transcript variant X24 XM_005246610.2:c. N/A Splice Donor Variant
NEB transcript variant X25 XM_005246611.2:c. N/A Splice Donor Variant
NEB transcript variant X26 XM_005246612.2:c. N/A Splice Donor Variant
NEB transcript variant X27 XM_005246613.2:c. N/A Splice Donor Variant
NEB transcript variant X31 XM_005246615.2:c. N/A Splice Donor Variant
NEB transcript variant X33 XM_005246616.1:c. N/A Splice Donor Variant
NEB transcript variant X35 XM_005246617.2:c. N/A Splice Donor Variant
NEB transcript variant X17 XM_006712541.2:c. N/A Splice Donor Variant
NEB transcript variant X20 XM_006712542.2:c. N/A Splice Donor Variant
NEB transcript variant X29 XM_011511225.2:c. N/A Splice Donor Variant
NEB transcript variant X34 XM_011511226.2:c. N/A Splice Donor Variant
NEB transcript variant X36 XM_011511227.2:c. N/A Splice Donor Variant
NEB transcript variant X6 XM_017004177.1:c. N/A Splice Donor Variant
NEB transcript variant X8 XM_017004178.1:c. N/A Splice Donor Variant
NEB transcript variant X16 XM_017004179.1:c. N/A Splice Donor Variant
NEB transcript variant X19 XM_017004180.1:c. N/A Splice Donor Variant
NEB transcript variant X21 XM_017004181.1:c. N/A Splice Donor Variant
NEB transcript variant X23 XM_017004182.1:c. N/A Splice Donor Variant
NEB transcript variant X28 XM_017004183.1:c. N/A Splice Donor Variant
NEB transcript variant X30 XM_017004184.1:c. N/A Splice Donor Variant
NEB transcript variant X32 XM_017004185.1:c. N/A Splice Donor 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: 101004 )
ClinVar Accession Disease Names Clinical Significance
RCV000174538.1 Nemaline myopathy 2 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 216496 C=0.99997 A=0.00001, T=0.00002
The Genome Aggregation Database European Sub 116998 C=0.99995 A=0.00002, T=0.00003
The Genome Aggregation Database Asian Sub 41392 C=1.0000 A=0.0000, T=0.0000
The Genome Aggregation Database American Sub 29946 C=1.0000 A=0.0000, T=0.0000
The Genome Aggregation Database African Sub 13916 C=1.0000 A=0.0000, T=0.0000
The Genome Aggregation Database Ashkenazi Jewish Sub 9232 C=1.000 A=0.000, T=0.000
The Genome Aggregation Database Other Sub 5012 C=1.000 A=0.000, T=0.000
Trans-Omics for Precision Medicine Global Study-wide 125568 C=0.99998 T=0.00002
The Exome Aggregation Consortium Global Study-wide 46508 C=1.0000 A=0.0000
The Exome Aggregation Consortium Europe Sub 25950 C=1.0000 A=0.0000
The Exome Aggregation Consortium Asian Sub 12822 C=1.0000 A=0.0000
The Exome Aggregation Consortium African Sub 5390 C=1.000 A=0.000
The Exome Aggregation Consortium American Sub 1944 C=1.000 A=0.000
The Exome Aggregation Consortium Other Sub 402 C=1.00 A=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 2 NC_000002.12:g.15...

NC_000002.12:g.151706880C=

NC_000002.12:g.15...

NC_000002.12:g.151706880C>A

NC_000002.12:g.15...

NC_000002.12:g.151706880C>T

GRCh37.p13 chr 2 NC_000002.11:g.15...

NC_000002.11:g.152563394C=

NC_000002.11:g.15...

NC_000002.11:g.152563394C>A

NC_000002.11:g.15...

NC_000002.11:g.152563394C>T

NEB RefSeqGene (LRG_202) NG_009382.2:g.326...

NG_009382.2:g.32608G=

NG_009382.2:g.326...

NG_009382.2:g.32608G>T

NG_009382.2:g.326...

NG_009382.2:g.32608G>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#.

3 Frequency, 4 SubSNP, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EGL ss947848036 Jan 23, 2014 (138)
2 EVA_EXAC ss1686546003 Apr 01, 2015 (144)
3 GNOMAD ss2733035750 Nov 08, 2017 (151)
4 TOPMED ss3326736402 Nov 08, 2017 (151)
5 The Exome Aggregation Consortium NC_000002.11 - 152563394 Jul 19, 2018 (151)
6 The Genome Aggregation Database NC_000002.11 - 152563394 Jul 19, 2018 (151)
7 Trans-Omics for Precision Medicine NC_000002.12 - 151706880 Jul 19, 2018 (151)
8 ClinVar RCV000174538.1 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
6435310, 2050485, ss1686546003, ss2733035750 NC_000002.11:152563393:C= NC_000002.12:151706879:C= (self)
207662655, ss947848036, ss3326736402 NC_000002.12:151706879:C= NC_000002.12:151706879:C= (self)
6435310, 2050485, ss1686546003, ss2733035750 NC_000002.11:152563393:C>A NC_000002.12:151706879:C>A (self)
2050485, ss2733035750 NC_000002.11:152563393:C>T NC_000002.12:151706879:C>T (self)
RCV000174538.1, 207662655, ss947848036, ss3326736402 NC_000002.12:151706879:C>T NC_000002.12:151706879: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.

2 citations for rs398124167
PMID Title Author Year Journal
23572184 Troponin activator augments muscle force in nemaline myopathy patients with nebulin mutations. de Winter JM et al. 2013 Journal of medical genetics
23757202 Free the data: one laboratory's approach to knowledge-based genomic variant classification and preparation for EMR integration of genomic data. Bean LJ et al. 2013 Human mutation

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