<p>I am using R to extract ClinVar classification of SNPs using rsid. Here's an example of my workflow:</p>
<p>Patient data:</p>
<div class="s-table-container"><table class="s-table">
<thead>
<tr>
<th style="text-align: left;">Sample</th>
<th style="text-align: left;">Func</th>
<th style="text-align: left;">Gene</th>
<th style="text-align: left;">Codon_Change</th>
<th style="text-align: left;">dbSNPv151_GRCh38</th>
<th style="text-align: left;">Chr</th>
<th style="text-align: right;">Start</th>
<th style="text-align: right;">End</th>
<th style="text-align: left;">Ref</th>
<th style="text-align: left;">Obs</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align: left;">Mary</td>
<td style="text-align: left;">missense_variant</td>
<td style="text-align: left;">SPINK5</td>
<td style="text-align: left;">Cga/Gga</td>
<td style="text-align: left;">rs199757347</td>
<td style="text-align: left;">chr5</td>
<td style="text-align: right;">148091214</td>
<td style="text-align: right;">148091214</td>
<td style="text-align: left;">C</td>
<td style="text-align: left;">G</td>
</tr>
</tbody>
</table></div>
<p>With this rsid rs199757347, <a href="https://www.ncbi.nlm.nih.gov/clinvar/?term=rs199757347" rel="nofollow noreferrer">two ClinVar classifications</a> were found with different codon changes, one is C &gt; G (Uncertain significance, missense variant) and the other one C &gt; T (Pathogenic, nonsense variant).</p>
<p>With the <code>rentrez</code> package in R, I can extract both ClinVar classifications:</p>
<pre class="lang-r prettyprint-override"><code>library(XML)
library(rentrez)

extract_from_esummary(
  entrez_summary(db = &quot;clinvar&quot;, 
                 id = entrez_search(db = &quot;clinvar&quot;, term = &quot;rs199757347&quot;)$ids, 
                 rettype='xml', 
                 parsed = F), 
  &quot;germline_classification&quot;
  )

               968176                               
description    &quot;Uncertain significance&quot;             
last_evaluated &quot;2022/01/01 00:00&quot;                   
review_status  &quot;criteria provided, single submitter&quot;
trait_set      data.frame,2                         
               351517                                                
description    &quot;Pathogenic&quot;                                          
last_evaluated &quot;2019/01/01 00:00&quot;                                    
review_status  &quot;criteria provided, multiple submitters, no conflicts&quot;
trait_set      data.frame,2 
</code></pre>
<p>However, only the classification &quot;Uncertain significance&quot; is relevant to my sample, how can I incorporate the alternative alleles in querying ClinVar with rsid? Or do you have a better way to query ClinVar with my sample data?</p>

CC BY-SA 4.0
2024-02-15T11:57:20.730Z
Do you absolutely need to use rsIDs? The problem isn't clinvar here, it is that the rsID describes two variants.
terdon
CC BY-SA 4.0
2024-02-15T12:02:30.920Z
@terdon, Yes I understand, that's why I wish to "incorporate" the info of ALT allele in the search. And based on my sample data, I think the most useful info for querying ClinVar is the rsID. Do you have other recommendations on querying ClinVar if I don't use rsID? Thank you!
benson23
CC BY-SA 4.0
2024-02-15T13:15:17.177Z
I am afraid not. I am spoiled, the company I work for has a [really good API](https://landing.varsome.com/varsome-api) and that's what I use, but it isn't a free product so any answer I post using it would only be helpful to our clients :/ However, my guess is that you should be able to get the nt change if you don't restrict the output to `germline_classification` only, so then you should be able to parse that to get what you need. Alternatively, if you can convert the rsIDs to HGVS notation (i.e. `NM_006846.4(SPINK5):c.652C>G` in your case), you can query using that.
terdon
<r><snp><wgs><entrez><rsid>
Different ClinVar classifications/SNPs are linked to the same rsid
# Different ClinVar classifications/SNPs are linked to the same rsid

(Asked by: username_0 on 2024-02-15)

I am using R to extract ClinVar classification of SNPs using rsid. Here's an example of my workflow:
Patient data:



Sample
Func
Gene
Codon_Change
dbSNPv151_GRCh38
Chr
Start
End
Ref
Obs




Mary
missense_variant
SPINK5
Cga/Gga
rs199757347
chr5
148091214
148091214
C
G



With this rsid rs199757347, two ClinVar classifications were found with different codon changes, one is C > G (Uncertain significance, missense variant) and the other one C > T (Pathogenic, nonsense variant).
With the rentrez package in R, I can extract both ClinVar classifications:
library(XML)
library(rentrez)

extract_from_esummary(
  entrez_summary(db = "clinvar", 
                 id = entrez_search(db = "clinvar", term = "rs199757347")$ids, 
                 rettype='xml', 
                 parsed = F), 
  "germline_classification"
  )

               968176                               
description    "Uncertain significance"             
last_evaluated "2022/01/01 00:00"                   
review_status  "criteria provided, single submitter"
trait_set      data.frame,2                         
               351517                                                
description    "Pathogenic"                                          
last_evaluated "2019/01/01 00:00"                                    
review_status  "criteria provided, multiple submitters, no conflicts"
trait_set      data.frame,2 

However, only the classification "Uncertain significance" is relevant to my sample, how can I incorporate the alternative alleles in querying ClinVar with rsid? Or do you have a better way to query ClinVar with my sample data?

**Tags:** r, snp, wgs, entrez, rsid
> **Comments:**
> **username_1**: Do you absolutely need to use rsIDs? The problem isn't clinvar here, it is that the rsID describes two variants.  
> **username_0**: @terdon, Yes I understand, that's why I wish to "incorporate" the info of ALT allele in the search. And based on my sample data, I think the most useful info for querying ClinVar is the rsID. Do you have other recommendations on querying ClinVar if I don't use rsID? Thank you!  
> **username_1**: I am afraid not. I am spoiled, the company I work for has a [really good API](https://landing.varsome.com/varsome-api) and that's what I use, but it isn't a free product so any answer I post using it would only be helpful to our clients :/ However, my guess is that you should be able to get the nt change if you don't restrict the output to `germline_classification` only, so then you should be able to parse that to get what you need. Alternatively, if you can convert the rsIDs to HGVS notation (i.e. `NM_006846.4(SPINK5):c.652C>G` in your case), you can query using that.  

---

## 0 answers

