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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.


Current Build 151

Released July 17, 2018

Homo sapiens
chr7:146438846 (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.

Variation Type
SNV Single Nucleotide Variation
C=0.03195 (4012/125568, TOPMED)
C=0.0285 (878/30782, GnomAD)
C=0.027 (137/5008, 1000G) (+ 2 more)
C=0.000 (1/3854, ALSPAC)
C=0.000 (0/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CNTNAP2 : Intron Variant
0 citations
Genomic View
See rs on genome

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 7 NC_000007.14:g.146438846T>C
GRCh37.p13 chr 7 NC_000007.13:g.146135938T>C
CNTNAP2 RefSeqGene NG_007092.2:g.327486T>C
Gene: CNTNAP2, contactin associated protein-like 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CNTNAP2 transcript NM_014141.5:c. N/A Intron Variant
CNTNAP2 transcript variant X1 XM_017011950.1:c. N/A Intron Variant

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.

Not Reported in ClinVar

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").

Study Population Group Sample Size Ref Allele Alt Allele
Trans-Omics for Precision Medicine Global Study-wide 125568 T=0.96805 C=0.03195
The Genome Aggregation Database Global Study-wide 30782 T=0.9715 C=0.0285
The Genome Aggregation Database European Sub 18470 T=0.9996 C=0.0004
The Genome Aggregation Database African Sub 8574 T=0.899 C=0.101
The Genome Aggregation Database East Asian Sub 1616 T=1.000 C=0.000
The Genome Aggregation Database Other Sub 982 T=1.00 C=0.00
The Genome Aggregation Database American Sub 838 T=1.00 C=0.00
The Genome Aggregation Database Ashkenazi Jewish Sub 302 T=1.00 C=0.00
1000Genomes Global Study-wide 5008 T=0.973 C=0.027
1000Genomes African Sub 1322 T=0.902 C=0.098
1000Genomes East Asian Sub 1008 T=1.000 C=0.000
1000Genomes Europe Sub 1006 T=0.999 C=0.001
1000Genomes South Asian Sub 978 T=1.00 C=0.00
1000Genomes American Sub 694 T=0.99 C=0.01
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=1.000 C=0.000
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=1.000 C=0.000

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 T= C Note
GRCh38.p7 chr 7 NC_000007.14:g.146438846T= NC_000007.14:g.14643884...


GRCh37.p13 chr 7 NC_000007.13:g.146135938T= NC_000007.13:g.14613593...


CNTNAP2 RefSeqGene NG_007092.2:g.327486T= NG_007092.2:g.327486T>C

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 Frequency, 18 SubSNP submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2140031 Oct 23, 2000 (88)
2 SC_JCM ss2563387 Nov 09, 2000 (92)
3 ILLUMINA ss160341247 Dec 01, 2009 (131)
4 1000GENOMES ss223393694 Jul 14, 2010 (132)
5 ILLUMINA ss480583205 Sep 08, 2015 (146)
6 TISHKOFF ss560375755 Apr 25, 2013 (138)
7 JMKIDD_LAB ss1075072601 Aug 21, 2014 (142)
8 1000GENOMES ss1327602252 Aug 21, 2014 (142)
9 EVA_DECODE ss1594511119 Apr 01, 2015 (144)
10 EVA_UK10K_ALSPAC ss1619464073 Apr 01, 2015 (144)
11 EVA_UK10K_TWINSUK ss1662458106 Apr 01, 2015 (144)
12 WEILL_CORNELL_DGM ss1928179452 Feb 12, 2016 (147)
13 HUMAN_LONGEVITY ss2298812465 Dec 20, 2016 (150)
14 GNOMAD ss2860460609 Nov 08, 2017 (151)
15 AFFY ss2986055043 Nov 08, 2017 (151)
16 ILLUMINA ss3022790731 Nov 08, 2017 (151)
17 TOPMED ss3547539431 Nov 08, 2017 (151)
18 ILLUMINA ss3636881909 Jul 20, 2018 (151)
19 1000Genomes NC_000007.13 - 146135938 Jul 20, 2018 (151)
20 The Avon Longitudinal Study of Parents and Children NC_000007.13 - 146135938 Jul 20, 2018 (151)
21 The Genome Aggregation Database NC_000007.13 - 146135938 Jul 20, 2018 (151)
22 Trans-Omics for Precision Medicine NC_000007.14 - 146438846 Jul 20, 2018 (151)
23 UK 10K study - Twins NC_000007.13 - 146135938 Jul 20, 2018 (151)

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).

Associated ID History Updated (Build)
rs1724484 Jan 18, 2001 (92)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss1594511119 NC_000007.12:145766870:T= NC_000007.14:146438845:T= (self)
39663406, 22074366, 201088367, 22074366, ss223393694, ss480583205, ss560375755, ss1075072601, ss1327602252, ss1619464073, ss1662458106, ss1928179452, ss2860460609, ss2986055043, ss3022790731, ss3636881909 NC_000007.13:146135937:T= NC_000007.14:146438845:T= (self)
378417347, ss2298812465, ss3547539431 NC_000007.14:146438845:T= NC_000007.14:146438845:T= (self)
ss2140031, ss2563387, ss160341247 NT_007914.15:6731560:T= NC_000007.14:146438845:T= (self)
ss1594511119 NC_000007.12:145766870:T>C NC_000007.14:146438845:T>C (self)
39663406, 22074366, 201088367, 22074366, ss223393694, ss480583205, ss560375755, ss1075072601, ss1327602252, ss1619464073, ss1662458106, ss1928179452, ss2860460609, ss2986055043, ss3022790731, ss3636881909 NC_000007.13:146135937:T>C NC_000007.14:146438845:T>C (self)
378417347, ss2298812465, ss3547539431 NC_000007.14:146438845:T>C NC_000007.14:146438845:T>C (self)
ss2140031, ss2563387, ss160341247 NT_007914.15:6731560:T>C NC_000007.14:146438845:T>C (self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs1358075

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