---
title: How to recalculate variants in phase that are called separately?
description: In the rare case variants, such as MNPs (multi-nucleotide polymorphisms) delinses, are split into smaller atomic SNVs (single nucleotide variants) or INDELs (insertions and deletions), they may need t
---
[Skip to content](https://docs.varsome.com/en/how-to-recalculate-close-by-variants-in-phase#main-content)
English
Show submenu for translations
[Submit a Support Request](https://docs.varsome.com/en/kb-tickets/new?hsLang=en) [Customer portal](https://docs.varsome.com/support-requests?hsLang=en)
[![varsome-new.png\]](https://docs.varsome.com/hs-fs/hubfs/varsome-new.png?height=40&name=varsome-new.png)](https://docs.varsome.com/en?hsLang=en)
- Editions
Show submenu for Editions
- [VarSome.com](https://landing.varsome.com/varsome)
- [VarSome Clinical](https://landing.varsome.com/varsome-clinical)
- [VarSome Premium](https://landing.varsome.com/varsome-premium)
- [VarSome API](https://landing.varsome.com/varsome-api)
- [VarSome Insights](https://landing.varsome.com/varsome-insights)
- About
Show submenu for About
- [The Company](https://saphetor.com/)
- [Contact Us](https://landing.varsome.com/contact)
- [Distributors](https://landing.varsome.com/distributors)
- [Become a Partner](https://landing.varsome.com/become-varsome-partner)
- [Community](https://varsome.com/community-contributions/)
- [Cite VarSome!](https://varsome.com/about/general/varsome-citations/)
- Resources
Show submenu for Resources
- [Datasources](https://varsome.com/datasources/)
- [Germline Classification](https://varsome.com/about/resources/germline-implementation/)
- [Somatic Classification](https://varsome.com/about/resources/somatic-implementation/)
- [CNV Classification](https://varsome.com/about/resources/sv-implementation/)
- [Help Center](https://docs.varsome.com/)
- [Library](https://landing.varsome.com/whitepapers)
- [IVDR](https://landing.varsome.com/ivdr-whitepaper)
- [Legal & Compliance](https://docs.varsome.com/en/legal-compliance)
- Blog
Show submenu for Blog
- [Platform Updates](https://updates.varsome.com/en)
- [Company News](https://news.varsome.com/en)
- [VarSome Annotated](https://blog.varsome.com/annotated)
Open main navigation
Close main navigation
- Editions
Show submenu for Editions
- [VarSome.com](https://landing.varsome.com/varsome)
- [VarSome Clinical](https://landing.varsome.com/varsome-clinical)
- [VarSome Premium](https://landing.varsome.com/varsome-premium)
- [VarSome API](https://landing.varsome.com/varsome-api)
- [VarSome Insights](https://landing.varsome.com/varsome-insights)
- About
Show submenu for About
- [The Company](https://saphetor.com/)
- [Contact Us](https://landing.varsome.com/contact)
- [Distributors](https://landing.varsome.com/distributors)
- [Become a Partner](https://landing.varsome.com/become-varsome-partner)
- [Community](https://varsome.com/community-contributions/)
- [Cite VarSome!](https://varsome.com/about/general/varsome-citations/)
- Resources
Show submenu for Resources
- [Datasources](https://varsome.com/datasources/)
- [Germline Classification](https://varsome.com/about/resources/germline-implementation/)
- [Somatic Classification](https://varsome.com/about/resources/somatic-implementation/)
- [CNV Classification](https://varsome.com/about/resources/sv-implementation/)
- [Help Center](https://docs.varsome.com/)
- [Library](https://landing.varsome.com/whitepapers)
- [IVDR](https://landing.varsome.com/ivdr-whitepaper)
- [Legal & Compliance](https://docs.varsome.com/en/legal-compliance)
- Blog
Show submenu for Blog
- [Platform Updates](https://updates.varsome.com/en)
- [Company News](https://news.varsome.com/en)
- [VarSome Annotated](https://blog.varsome.com/annotated)
- English
Show submenu for translations
- [Submit a Support Request](https://docs.varsome.com/en/kb-tickets/new)
- [Customer portal](https://docs.varsome.com/support-requests)
- [Contact us](https://docs.varsome.com/en/kb-tickets/new)
[Contact us](https://docs.varsome.com/en/kb-tickets/new?hsLang=en)
How can we help you?
- There are no suggestions because the search field is empty.
1. [VarSome Help Center](https://docs.varsome.com/en?hsLang=en)
2. [FAQ & Troubleshooting](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en)
3. [General](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#general)
# How to recalculate variants in phase that are called separately?
In the rare case variants, such as MNPs (multi-nucleotide polymorphisms) delinses, are split into smaller atomic SNVs (single nucleotide variants) or INDELs (insertions and deletions), they may need to be recalculated into a single MNP. This process is important for accurate classification, especially when determining if two variants are in [phase](https://docs.varsome.com/en/phasing?hsLang=en) or are independent. This article explains how to recalculate split variants into a single MNP using VarSome Clinical, with a detailed example from a clinical case.
---
### **Case example: ENG gene variants**
Consider a case where we have two variants in the **ENG** gene, and the end user is seeking confirmation about whether these two variants are in phase and should be analyzed together or if they are independent in the **hg19** reference genome:
- **Variant 1:** [NM\_001114753.3:c.466\_471del](https://varsome.com/variant/hg19/NM_001114753.3%3Ac.466_471del?annotation-mode=germline)(p.Ile156\_Thr157del)
- **Variant 2:** [NM\_001114753.3:c.445\_458del](https://varsome.com/variant/hg19/NM_001114753.3%3Ac.445_458del?annotation-mode=germline)(p.Trp149GlyfsTer8)
### **Step 1: Identifying other potential involved variants**
Before determining whether the variants are in phase, it is useful to check for other variants in the genomic neighborhood that might be involved. Here’s how to identify them:
1. **Nearby Variants card:** In VarSome Clinical, navigate to the [**Nearby Variants**](https://docs.varsome.com/en/clinical-cards?hsLang=en) section in the clinical card for the selected variant. This will display variants in the genomic neighborhood of your variant.
2. **Not affected by sample filters:** This list will not be affected by any filters applied to the sample, so it provides a comprehensive look at other variants in the area.
3. **Check PGT and PID for nearby variants:** By reviewing these nearby variants, you can assess if any of them share the same **PGT** and **PID** attributes, suggesting that they might also be in phase or linked to the variants in question.
### **Step 2: Determine if the variants are in phase**
To determine if the two variants are in phase, follow these steps within VarSome Clinical:
1. **Search for VCF attributes PGT and PID:**
- **PGT (Physical Phasing Haplotype Information):** Describes how the alternate alleles are phased relative to one another (e.g., 0|1 or 1|0).
- **PID (Physical Phasing ID Information):** A unique ID within a sample that connects records within a phasing group.
2. **Comparing PGT and PID:** In VarSome Clinical, these attributes will appear in the variant details (as shown in the example image below). Compare the **PGT** and **PID** values for both variants.
[](https://docs.varsome.com/hubfs/image-png-Feb-18-2025-05-29-36-1724-PM.png?hsLang=en)
**Key rule:** If two variants share the same **PGT** and **PID**, they are not independent, meaning they are on the same haplotype and therefore in phase. This means the variants should not be analyzed separately.
3. **Conclusion:** In this case, if the **PGT** and **PID** for both variants are identical, they are in phase. As a result, they should be recalculated into a single variant.
### **Step 3: Recalculate the variant**
Once you determine that the variants are in phase, you need to recalculate the two split variants into a single MNP. Here’s how to do that:
1. **Reference sequence:** Start with the reference sequence where the two variants occur:
`GGTGATGGGGCCCCTCTCAGCTGCCCA`
- **Variant 1 (c.466\_471del)** is the **underlined** first 6 nucleotides.
- **Variant 2 (c.445\_458del)** is the second **underlined** segment of 14 nucleotides.
2. **Resulting sequence after deletions:** These two deletions occur at the same time, which means the combined result is the deletion of the bases from both variants. The resulting sequence will be:
`GGGGCCC`
3. **Formulate the query:** Use the resulting sequence to create a new VarSome query:
`chr9:130588841:GGTGATGGGGCCCCTCTCAGCTGCCCA:GGGGCCC`
This will give you the [merged variant](https://varsome.com/variant/hg19/chr9%3A130588841%3AGGTGATGGGGCCCCTCTCAGCTGCCCA%3AGGGGCCC?annotation-mode=germline).
4. **Recalculated variant:** The recalculated variant is now:
`ENG(NM_001114753.3):c.445_469delinsGGGCC p.(Trp149GlyfsTer6)`
This is the single MNP that combines the two original variants.
Using the **PGT** and **PID** attributes in VarSome Clinical, you can easily determine if variants are in phase and merge them accordingly. The recalculation process helps ensure a more accurate analysis of genetic variants.
- [Registration & Billing](https://docs.varsome.com/en/registration-billing?hsLang=en#main-content)
- [User account management](https://docs.varsome.com/en/registration-billing?hsLang=en#user-account-management)
- [Storage management](https://docs.varsome.com/en/registration-billing?hsLang=en#storage-management)
- [Pricing and Billing](https://docs.varsome.com/en/registration-billing?hsLang=en#pricing-and-billing)
- [VarSome Clinical Tokens](https://docs.varsome.com/en/registration-billing?hsLang=en#varsome-clinical-tokens)
- [Management of Samples and Analyses](https://docs.varsome.com/en/management-of-samples-and-analyses?hsLang=en#main-content)
- [Uploading files](https://docs.varsome.com/en/management-of-samples-and-analyses?hsLang=en#uploading-files)
- [Managing Samples](https://docs.varsome.com/en/management-of-samples-and-analyses?hsLang=en#managing-samples)
- [Managing Workflows](https://docs.varsome.com/en/management-of-samples-and-analyses?hsLang=en#managing-workflows)
- [Launching analyses](https://docs.varsome.com/en/management-of-samples-and-analyses?hsLang=en#launching-analyses)
- [Analysis of the results](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en#main-content)
- [Analyses](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en#analyses)
- [Results](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en#results)
- [Filters](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en#filters)
- [Reporting](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en#reporting)
- [Quality Control](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en#quality-control)
- [Legal & compliance](https://docs.varsome.com/en/legal-compliance?hsLang=en)
- [FAQ & Troubleshooting](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#main-content)
- [Troubleshooting](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#troubleshooting)
- [General](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#general)
- [Filters](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#filters)
- [User Interface](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#user-interface)
- [Pipelines](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#pipelines)
- [Features](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#features)
- [Scientific articles](https://docs.varsome.com/en/scientific-articles?hsLang=en)
- [VarSome API](https://docs.varsome.com/en/varsome-api?hsLang=en)
[](https://varsome.com)
**Resources**
[Query Examples](https://varsome.com/about/resources/examples/)
[Germline Classification](https://varsome.com/about/resources/germline-implementation/)
[Somatic Classification](https://varsome.com/about/resources/somatic-implementation/)
[White Papers & Other Resources](https://varsome.com/library/)
[Cite VarSome](https://varsome.com/about/general/varsome-citations/)
[System Status](https://status.saphetor.com/)
[Help Center](https://docs.varsome.com/en?hsLang=en)
**Legal**
[Terms of Use](https://varsome.com/information/legal/terms/)
[Privacy Policy](https://varsome.com/information/legal/privacy/)
[Information Security](https://varsome.com/information/legal/information-security/)
Copyright © 2025, Saphetor SA