Genetic Counselling Resources

This page lists resources and recommendations on genetic counseling and the interpretation of specialized genetic and biochemical tests.

Cardiogenetics

Cardioboost - In silico tool for cardiomyopathies and arrhythmias

Morales et al., 2020 - Criteria for dilated cardiomyopathies

Kelly et al., 2018 - ACMG criteria adapted for MYH7 gene by Clingen expert panel

General criteria for classifying variants

Houge et al., 2022 - ABC variant classification system 

Clingen - Clingen Recommendations (Updates on ACMG/AMP criteria)

Nykamp et al., 2017 - Sherloc criteria

Richards et al., 2015 - ACMG/AMP criteria

Genetic testing

Association for Clinical Genomic Science

Miller et al., 2023 - ACMG recommendations on secondary findings - ACMG SF v3.2.

ACMG, 2022 - ACMG recommendations on detection of structural variants by next-generation sequencing.

Deans et al., 2022 - ESHG Guidelines on Genomic Test Reports

Gaudio, 2020 - ACMG recommendations for diagnostic testing for uniparental disomy

SBGM, 2020 - SBGM statement on genetic tests

Bush, 2018 - ACMG recommendations for pre-test counseling for teens and older children

Genetic variant databases

Database of Genomic Variants

MitoDB

Clinvitae  - Invitae variant database

Gnomad - Population database. Helps in assessing the frequency of the variant in a "normal" population

Clinvar - Public variant database with independently submitted laboratory interpretations of pathogenicity

Interpretation of biochemical tests

https://hmdb.ca/ - Metabolome data listing conditions under which each metabolite is expressed

IEM Base - Allows the search for inborn errors of metabolism described by metabolites or signs and symptoms

Prenatal genetic counseling

Gregg, 2021 - ACMG recommendations for screening for autosomal recessive and X-linked conditions

Grody, 2013 - ACMG Recommendations for Assessing Prenatal/Preconception Carrier Status

Prior, 2008 - ACMG recommendations for assessing carrier status for spinal muscular atrophy

Resources for variant interpretation

Varsome - Facilitates classification by ACMG criteria. It accepts .vcf and .fastq files only in the paid version.

Franklin - Facilitates classification by ACMG criteria. It accepts both variants and .vcf files.

Genetic Variant Interpretation Tool - ACMG criteria checklist

Uniprot - Allows evaluation of the domain in which the variant occurs.

ProteinPaint - Facilitates visualization of hotspots in the gene.

Mutalyzer - Allows you to check the variant description. Similar to VariantValidator.

UCSC Genome Browser - Useful tool for localizing the variant in the genome. Includes a wide range of customizable annotations.

VariantValidator - Enables validation, mapping and formatting of sequence variant descriptions. Similar to Mutalyzer.

 

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