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<div class="pre-content"><div><div class="bk_prnt"><p class="small">NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.</p><p>SNP FAQ Archive [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2005-. </p></div><div class="messagearea bk_noprnt" style="margin-bottom:1.3846em "><ul class="messages"><li class="warn icon"><span class="icon">This publication is provided for historical reference only and the information may be out of date.</span></li></ul></div><div class="bk_prnt"><p style="color:red;"><strong>This publication is provided for historical reference only and the information may be out of date.</strong></p></div><div class="iconblock clearfix whole_rhythm no_top_margin bk_noprnt"><a class="img_link icnblk_img" title="Table of Contents Page" href="/books/n/helpsnpfaq/"><img class="source-thumb" src="/corehtml/pmc/pmcgifs/bookshelf/thumbs/th-helpsnpfaq-lrg.png" alt="Cover of SNP FAQ Archive" height="100px" width="80px" /></a><div class="icnblk_cntnt eight_col"><h2>SNP FAQ Archive [Internet].</h2><a data-jig="ncbitoggler" href="#__NBK573518_dtls__">Show details</a><div style="display:none" class="ui-widget" id="__NBK573518_dtls__"><div>Bethesda (MD): <a href="https://www.ncbi.nlm.nih.gov/" ref="pagearea=page-banner&targetsite=external&targetcat=link&targettype=publisher">National Center for Biotechnology Information (US)</a>; 2005-.</div></div><div class="half_rhythm"><ul class="inline_list"><li style="margin-right:1em"><a class="bk_cntns" href="/books/n/helpsnpfaq/">Contents</a></li></ul></div></div><div class="icnblk_cntnt two_col"><div class="pagination bk_noprnt"><a class="active page_link prev" href="/books/n/helpsnpfaq/Rprt_Field_Definitio/" title="Previous page in this title">< Prev</a><a class="active page_link next" href="/books/n/helpsnpfaq/Rprt_Sequence_Format/" title="Next page in this title">Next ></a></div></div></div></div></div>
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<div class="main-content lit-style" itemscope="itemscope" itemtype="http://schema.org/CreativeWork"><div class="meta-content fm-sec"><h1 id="_NBK573518_"><span class="title" itemprop="name">SNP Class Definitions</span></h1><p class="small">Created: <span itemprop="datePublished">July 7, 2005</span>; Last Update: <span itemprop="dateModified">February 18, 2014</span>.</p><p><em>Estimated reading time: 4 minutes</em></p></div><div class="jig-ncbiinpagenav body-content whole_rhythm" data-jigconfig="allHeadingLevels: ['h2'],smoothScroll: false" itemprop="text"><ul class="simple-list"><li><h4>Functional Class</h4></li><li><p><a href="#Rprt_SNP_Class_Defin.i_do_not_understand">I do not understand the meaning of the "Function" category or any of its components (e.g. synonymous, contig reference, nonsynonymous)?</a></p></li><li><p><a href="#Rprt_SNP_Class_Defin.what_does_it_mean_w">What does it mean when an SNP is labeled “synonymous” or “non-synonymous”?</a></p></li><li><p><a href="#Rprt_SNP_Class_Defin.i_noticed_in_the_do">I noticed in the documentation where "coding nonsynonymous" is mentioned as a SNP function class, yet, I don’t think I’ve ever seen it used. Instead I see the term "missense".</a></p></li><li><p><a href="#Rprt_SNP_Class_Defin.where_are_descripti">Where are descriptions of your functional classifications located?</a></p></li><li><p><a href="#Rprt_SNP_Class_Defin.please_clarify_the">Please clarify the definition for functional class code 8 (“reference”).</a></p></li><li><p><a href="#Rprt_SNP_Class_Defin.what_is_the_definit">What is the definition for the “Locus region” functional class?</a></p></li></ul><ul class="simple-list"><li><h4>Variation Class</h4></li><li><p><a href="#Rprt_SNP_Class_Defin.the_alleles_for_rs1">The alleles for rs1611430 are reported A/G/T, yet the variation class is SNP. I thought this classification was reserved for biallelic SNPs, and that tri- and multi-alleles were classified as MNPs.</a></p></li><li><p><a href="#Rprt_SNP_Class_Defin._snpclass1_is_a_ter">“snpclass1”, is a term I found in the SNP report header. What is its definition?</a></p></li></ul><div id="Rprt_SNP_Class_Defin.Functional_Class"><h2 id="_Rprt_SNP_Class_Defin_Functional_Class_">Functional Class</h2><div><h4 id="Rprt_SNP_Class_Defin.i_do_not_understand">I do not understand the meaning of the "Function" category or any of its components (e.g. synonymous, contig reference, nonsynonymous)?</h4><blockquote><p>The NCBI handbook has <a href="/books/n/handbook/ch5/#ch5.ch5_4_11_1">documentation</a> that should address your questions. Below is an excerpt from that document that should address your question:</p><p>“...[fxn-class] defines variation functional classes. We base class on the relationship between a variation and any local gene features. When a variation is near a transcript or in a transcript interval but not in the coding region, then we define the functional class by the position of the variation relative to the structure of the aligned transcript. In other words, a variation may be near a gene (locus region), in a UTR (mrna-utr), in an intron (intron), or in a splice site (splice site). If the variation is in a coding region, then the functional class of the variation depends on how each allele may affect the translated peptide sequence.</p><p>Typically, one allele of a variation will be the same as the contig (contig reference), and the other allele will be either a synonymous change or a nonsynonymous change. In some cases, one allele will be a synonymous change, and the other allele will be a nonsynonymous change. If any allele is a nonsynonymous change, then the variation is classified as a nonsynonymous variation. Otherwise, the variation is classified as a synonymous variation.</p><p>The Four Basic Outcomes When a Variation Is in Coding Sequence</p><ul><li class="half_rhythm"><div>The allele is the same as the contig (contig reference) and hence causes no change to the translated sequence.</div></li><li class="half_rhythm"><div>The allele, when substituted for the reference sequence, yields a new codon that encodes the same amino acid. This is termed a synonymous substitution.</div></li><li class="half_rhythm"><div>The allele, when substituted for the reference sequence, yields a new codon that encodes a different amino acid. This is termed a nonsynonymous substitution.</div></li><li class="half_rhythm"><div>A problem with the annotated coding region feature prohibits conceptual translation. In this case, we note the variation class as coding, based solely on position.</div></li></ul><p>Because functional classification is defined by positional and sequence parameters, two facts emerge: (a) if a gene has multiple transcripts because of alternative splicing, then a variation may have several different functional relationships to the gene; and (b) if multiple genes are densely packed in a contig region, then a variation at a single location in the genome may have multiple, potentially different, relationships to its local gene neighbors.” <b>(3/14/05)</b></p></blockquote></div><div><h4 id="Rprt_SNP_Class_Defin.what_does_it_mean_w">What does it mean when an SNP is labeled “synonymous” or “non-synonymous”?</h4><blockquote><p>The terms “synonymous” and “non-synonymous” are used for SNPs that are in predicted protein coding regions (i.e., exons of genes). Synonymous SNPs are those SNPs that have different alleles that encode for the same amino acid. Non-synonymous SNPs are SNPs that have different alleles that encode different amino acids. For further details, I recommend querying for “genetic code” or “protein translation” at the <a href="/entrez/query.fcgi?db=Books" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">NCBI books website</a>.</p></blockquote></div><div><h4 id="Rprt_SNP_Class_Defin.i_noticed_in_the_do">I noticed in the documentation where "coding nonsynonymous" is mentioned as a SNP function class, yet, I don’t think I’ve ever seen it used. Instead I see the term "missense".</h4><blockquote><p>In ftp reports for older builds, we did use the term “nonsynonymous” to as a function class. Then about a year ago, the functional class code became more sophisticated so that it could describe the type of nonsynonymous change the SNP caused: “missense”, “nonsense” or “frameshift”.</p><p>So “”missense”, “nonsense”, and “frameshift” are types of nonsynonymous change a variation can cause. (<b>07/15/08</b>)</p></blockquote></div><div><h4 id="Rprt_SNP_Class_Defin.where_are_descripti">Where are descriptions of your functional classifications located?</h4><blockquote><p>They are located in the <a href="ftp://ftp.ncbi.nlm.nih.gov/snp/specs/docsum_2005.asn" ref="pagearea=body&targetsite=external&targetcat=link&targettype=ftp">asn docsum</a>. The portion of the docsum which answers your question is below:</p><pre>NSE-FxnSet ::= SEQUENCE {<br /><br />locusid INTEGER, locus-id of gene as aligned to contig <br /> SNPContigLocusId.locus_id<br />symbol VisibleString OPTIONAL, symbol (official if present in LocusLink) of gene<br /> SNPContigLocusId.locus_symbol<br />mrna-acc VisibleString OPTIONAL, mRNA accession if variation in transcript <br /> SNPContigLocusId.mrna_acc<br />prot-acc VisibleString OPTIONAL, protein accession if variation in coding region<br /> interval SNPContigLocusId.protein_acc<br /><br />fxn-class-contig ENUMERATED {<br />locus-region (1), variation in region of gene, but not in transcript<br /> SNPContigLocusId.fxn_class<br />coding (2), variation in coding region of gene, assigned if the <br /> allele-specific class is unknown <br />coding-synon (3) no change in peptide for allele with respect to <br /> contig sequence **allele specific class**<br />coding-nonsynon (4), change in peptide with respect to contig sequence <br /> **allele-specific class**<br />mrna-utr (5), variation in transcript, but not in coding region interval<br />intron (6), variation in intron, but not in first 2 or last 2 bases <br /> of intron<br />splice-site (7), variation in first 2 or last 2 bases of intron<br />reference (8), allele observed in reference contig sequence <br /> **allele-specific class**<br />exception (9) variation in coding region with exception raised on<br /> alignment. This occurs when protein with gap in sequence is<br /> aligned back to contig sequence. variations 3' of the gap <br /> have undefined functional inference.</pre></blockquote></div><div><h4 id="Rprt_SNP_Class_Defin.please_clarify_the">Please clarify the definition for functional class code 8 (“reference”).</h4><blockquote><p>The word "reference" is used in two different contexts in dbSNP:</p><p>The first context for "reference" refers to the NCBI reference genome assembly, as opposed to alternative assemblies such as Celera.</p><p>The second context for "reference" is the "cds-reference" which is used as a functional class code (explained below).</p><p>I will use <a href="/snp/?term=268" class="bk_tag" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=snp">rs268</a> as an example of "cds-reference". <a href="/SNP/snp_ref.cgi?rs=268" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">rs268</a> has an A/G variation, which maps to reference contig <a href="/nuccore/51466871" class="bk_tag" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=nuccore">NT_030737</a> at position 7658457. The contig at this position has the allele "A". This SNP can have either an "A" or a "G" allele, and when the allele happens to be "G", it will cause a non-synonymous coding change. So in the SNP functional class context, "cds-reference" just means the "allele on the contig" since synonymous and non-synonymous alleles are relative to the contig. Please note: <a href="/snp/?term=268" class="bk_tag" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=snp">rs268</a> also maps to Celera contig <a href="/nuccore/89028628" class="bk_tag" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=nuccore">NW_923907</a>, which also has the "A" allele at this position. (<b>12/28/07</b>)</p></blockquote></div><div><h4 id="Rprt_SNP_Class_Defin.what_is_the_definit">What is the definition for the “Locus region” functional class?</h4><blockquote><p>Please see <a href="/books/n/handbook/ch5/#ch5.ch5_t5">Table 5</a> (refSNP Function Code Table) in the dbSNP section of the online NCBI handbook. <b>(5/18/05)</b></p></blockquote></div></div><div id="Rprt_SNP_Class_Defin.Variation_Class"><h2 id="_Rprt_SNP_Class_Defin_Variation_Class_">Variation Class</h2><div><h4 id="Rprt_SNP_Class_Defin.the_alleles_for_rs1">The alleles for <a href="/snp/?term=1611430" class="bk_tag" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=snp">rs1611430</a> are reported A/G/T, yet the variation class is SNP. I thought this classification was reserved for biallelic SNPs, and that tri- and multi-alleles were classified as MNPs.</h4><blockquote><p>MNPs in dbSNP are variations that have alleles with multiple nucleotides like AT/GT.(<b>6/8/07</b>)</p></blockquote></div><div><h4 id="Rprt_SNP_Class_Defin._snpclass1_is_a_ter">“snpclass1”, is a term I found in the SNP report header. What is its definition?</h4><blockquote><p>The snpclass values indicate the type of SNP using a classification scheme that is also <a href="ftp://ftp.ncbi.nlm.nih.gov/snp/specs/docsum_2005.asn" ref="pagearea=body&targetsite=external&targetcat=link&targettype=ftp">described in the spec file</a>.</p><div id="Rprt_SNP_Class_Defin.Tc" class="table"><p class="large-table-link" style="display:none"><span class="right"><a href="/books/NBK573518/table/Rprt_SNP_Class_Defin.Tc/?report=objectonly" target="object">View in own window</a></span></p><div class="large_tbl" id="__Rprt_SNP_Class_Defin.Tc_lrgtbl__"><table><thead><tr><th id="hd_h_Rprt_SNP_Class_Defin.Tc_1_1_1_1" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">Type of variation</th><th id="hd_h_Rprt_SNP_Class_Defin.Tc_1_1_1_2" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">SubSNP.subsnp_class</th></tr></thead><tbody><tr><td headers="hd_h_Rprt_SNP_Class_Defin.Tc_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">Snp (1)</td><td headers="hd_h_Rprt_SNP_Class_Defin.Tc_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">True single nucleotide polymorphism</td></tr><tr><td headers="hd_h_Rprt_SNP_Class_Defin.Tc_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">in-del (2)</td><td headers="hd_h_Rprt_SNP_Class_Defin.Tc_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">Insertion deletion polymorphism; deletions<br />represented by '-' in allele string</td></tr><tr><td headers="hd_h_Rprt_SNP_Class_Defin.Tc_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">het (3)</td><td headers="hd_h_Rprt_SNP_Class_Defin.Tc_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">Variation has unknown sequence composition<br />but is observed to be heterozygous</td></tr><tr><td headers="hd_h_Rprt_SNP_Class_Defin.Tc_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">microsat (4)</td><td headers="hd_h_Rprt_SNP_Class_Defin.Tc_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">Microsatellite/simple sequence repeat</td></tr><tr><td headers="hd_h_Rprt_SNP_Class_Defin.Tc_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">named (5)</td><td headers="hd_h_Rprt_SNP_Class_Defin.Tc_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">Allele sequences defined by name tag instead of raw sequence, e.g., (Alu)/-</td></tr><tr><td headers="hd_h_Rprt_SNP_Class_Defin.Tc_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">no-variation (6)</td><td headers="hd_h_Rprt_SNP_Class_Defin.Tc_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">Submission reports invariant region in surveyed sequence</td></tr><tr><td headers="hd_h_Rprt_SNP_Class_Defin.Tc_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">mixed (7)</td><td headers="hd_h_Rprt_SNP_Class_Defin.Tc_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">Mixed class</td></tr><tr><td headers="hd_h_Rprt_SNP_Class_Defin.Tc_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">mnp (8)</td><td headers="hd_h_Rprt_SNP_Class_Defin.Tc_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">Multiple nucleotide polymorphism (all alleles same length, where length >1)</td></tr></tbody></table></div></div></blockquote></div></div><div id="bk_toc_contnr"></div></div></div>
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