Mitomap and Variable Strength for ACMG now available in VarSome

Posted by Tomas Kucera on Dec 11, 2019 4:04:21 PM

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We are releasing Mitomap and Variable Strength for ACMG Criteria for the free VarSome.com.

Mitomap

MitoMap [1] has been incorporated into VarSome.com and can now be used as a source of clinical evidence for mitochondrial DNA.

Variable Strength for ACMG Criteria

Users can manually adjust the strength of individual rules in the ACMG annotation.

VarSome's automated ACMG annotation leverages this as follows:

  • Clinical Evidence rules PP5 and BP6 may be increased from Supporting to Very Strong if reviewed by an expert committee or multiple VarSome.com users have submitted evidence. This is helpful in highlighting a number of well-known pathogenic variants.

ACMG PP5 Explained

  • Synonymous PS1 and alternative PM5 amino-acid rules may be downgraded to Moderate, respectively Supporting, if the clinical evidence for the alternative known-pathogenic variant is not confirmed using VarSome's ACMG classification. VarSome has also improved the behavior of these rules if the amino-acids straddle a splice site.
ACMG PM5 Explained

These changes will only be applied to VarSome.com, for the moment, but we expect to be releasing them for VarSome Clinical, in the near future.

Example

The following variant related to Myopathy would be rated Uncertain Significance without the additional weighting of the clinical evidence for PP5.

ACMG PP5

This example also highlights the benefit of the many VarSome.com users contributing to the platform.

In conclusion

As ever, we hope that you find VarSome.com useful, and we are continually striving to improve the platform. Do please contact us if you notice any issues or have suggestions on how to improve the platform.

Presenting VarSome Clinical

Learn about VarSome Clinical

References

[1] https://www.mitomap.org/MITOMAP

 

Topics: Platform Updates

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