CanVar-UK

v2.2 (version history)
CanVar-UK datasets

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CanVar-UK

Nearly all data on CanVar-UK is accessible without registration.

Registration and membership of the CanVar-UK community grants access to the discussion forum, enabling facility for variant-level email enquiries to the whole CanVar-UK community as well as viewing of the variant-level discussions and provisional classifications.

Membership of the CanVar-UK community was previously restricted to UK NHS scientists/clinicians but has now been extended internationally to those whose work relates to or involves clinical diagnostics.

If you are a UK NHS scientist or clinician, please use your NHS email address when registering to enable access to laboratory-specific breakdown of UK National Laboratory Data submitted to PHE/NHSD.

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BRCA1 c.5207T>C p.(Val1736Ala)

Select a gene: Type a variant:

Gene-Specific Information

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Gene:

Chromosome:

Clinical transcript (RefSeq):

Clinical transcript (Ensembl):

Number of bases in cDNA:

Number of amino acids:

VCEP guidance

LSDs

PVS1: NMD

PVS1: Splicing

PS3/BS3: Functional assays

PM1/PP2: Constraint/Domains

PP5/BP6 : Reputable source

PP4/PS4: Case-control/Phenotype data)

PM3/BP2: Biallelic Variants

PM2/BA1/BS1: Allele frequency

BP1: Missense-benign

PS1/PM5: Other variants

PP3/BP4: In silico

PM4: Length change

PP1/BS2/BS4: Segregation

PM6/PS2: De novo

BP3/BP7: Synonymous/In-frame

BS2/BP5: Observed in controls/Alternative disease cause

Summary

Genome version	hg19
Gene
Ensembl transcript
RefSeq transcript
Chromosome
Genomic position (hg19)
Genomic position (hg38)
Reference allele
Variant allele
HGVS cDNA
HGVS (protein)
HGVS (protein, 1-letter)
Exon
rsID
Exon/Intron
Variant location
Variant type
Variant coding effect
cDNA position
Intronic position
Codon number
First/Last 3 bases of exon

Other Classifications

HGMD classification (2015)
DMuDB classification (2015)
UMD classification (2015)

Literature Links

Google Scholar Google Search PubMed

Database Links

ClinVar VarSome LOVD cBioPortal

ClinVar Status

Variant	Interpretation	Review Status	Last Evaluated

>> PM5: other variants at this codon (live retrieval may take a few seconds)

Variant	Protein Change	ClinVar Interpretation	ClinVar Status	REVEL score

In Silico Predictions

Missense/nonsense predictions

REVEL [0-1]
BayesDel (no AF)
BayesDel (add AF)
CADD v1.4 scaled score [0-99]
CADD v1.4 raw score
CADD v1.6 (CADD-Splice) scaled score [0-99]
CADD v1.6 (CADD-Splice) raw score
Gene-specific AlignGVGD class
Gene-specific AlignGVGD variation (GV)
Gene-specific AlignGVGD deviation (GD)
AlignGVGD class
AlignGVGD variation (GV)
AlignGVGD deviation (GD)
SIFT prediction
SIFT weight
SIFT median
PolyPhen-2 HumVar prediction
PolyPhen-2 HumVar probability of being damaging
PolyPhen-2 HumVar estimated FDR
PolyPhen-2 HumDiv prediction
PolyPhen-2 HumDiv probability of being damaging
PolyPhen-2 HumDiv estimated FDR
SuSPect score [0-100]
MAPP prediction
MAPP p-value
MAPP p-value median

SwissProt features

Description
Type

Conservation

No. of orthologues in alignment
No. of conserved residues in alignment
BLOSUM62

Splicing predictions

Distance to nearest splice site
Nearest splice site
Variant type
SpliceAI delta score (acceptor gain)
SpliceAI delta score (acceptor loss)
SpliceAI delta score (donor gain)
SpliceAI delta score (donor loss)

Control Frequency

gnomAD Population Frequencies (v2.1.1 - Jan. 2019)

gnomAD v2.1.1
gnomAD v2.1.1 non-cancer
gnomAD v2.1.1 non-cancer female

	Allele Count	Homoz.	Alleles sequenced	Individuals sequenced	WES in full dataset
European (Non-Finnish)
Latino
South Asian
European (Finnish)
East Asian
African
Ashkenazi Jewish
Other
Total

UK Biobank Population Frequencies (retrieved Jan. 2023)

Frequencies of non-base-substitution small variants in UK Biobank

UK Biobank (all participants)
UK Biobank (female-only)

	Allele Count	Homoz.	Alleles sequenced	Individuals sequenced	WES in full dataset
White
Asian
Black
Chinese
Mixed
Other
Total

1000 Genomes Project - phase 3 (2.5KG)

Hover over to see full population name

	All	Sub-population
Genotype count [ALL] (1KG)
MAF [ALL] (1KG)
size [ALL] (1KG)

Case Frequency

UK diagnostic labs (Release date: July 2023)

Total proband count
Total probands tested
White eth. (use as NFE): total proband count
White eth. (use as NFE): total probands tested

Database Sources	Number of times reported
LOVD3 (2019)
BIC (2015)
DMuDB
UMD

Genetic Epidemiology

Easton et al., Am J Hum Genet. 2007
Combined LLR (Easton LLR/ACMG LLR)
Family LLR (Easton LLR/ACMG LLR)
Co-occurrence LLR (Easton LLR/ACMG LLR)
Segregation LLR (Easton LLR/ACMG LLR)
Odds of causality (Easton)
Odds of neutrality (Easton)

IARC: Vallee et al., Hum Mutat. 2012
Product (IARC LR/ACMG LLR):
Segregation (IARC LR/ACMG LLR):
Pathology (IARC LR/ACMG LLR):
Family (IARC LR/ACMG LLR):
Co-occurrence (IARC LR/ACMG LLR):

Parsons et al., Human Mutation, 2019
Combined (Parsons LR/ACMG LLR):
Segregation (Parsons LR/ACMG LLR):
Pathology (Parsons LR/ACMG LLR):
Co-occurrence (Parsons LR/ACMG LLR):
Family history (Parsons LR/ACMG LLR):
Case-control (Parsons LR/ACMG LLR):

Garrett et al., Genetics in Medicine, 2021 (Total cases assembled: 6,118 (SDHB), and 5,847 (SDHD))
Birmingham (2000-2020)
Leeds (2015-2020)
France (2001-2010)
USA (2012-2020)
The Cancer Genome Atlas
Total case count

Caputo et al., AJHG, 2021
Combined (Caputo LR/ACMG LLR)
Co-segregation (Caputo LR/ACMG LLR)
Co-occurrence (Caputo LR/ACMG LLR)
Family history (Caputo LR/ACMG LLR)
Pathology (Caputo LR/ACMG LLR)

Li et al., Genet Med, 2020
Likelihood Ratio (Li LLR/ACMG LLR)

Functional Analysis

Click here to view the current evidence strengths applicable for functional assays, as quantified by CanVIG-UK. Assays with data currently stored in CanVar-UK are listed here.

Bouwman et al., 2020
Probability deleterious (cisplatin)
Prediction (cisplatin)
Probability deleterious (olaparib)
Prediction (olaparib)
Probability deleterious (DR-GFP)
Prediction (DR-GFP)

Fernandes et al., 2019
Functional class (fClass)
Functional class (fClass) category

Petitalot et al., 2019
Classification

Findlay et al., 2018
Function score
Function probability
Functional classification
Mean RNA score

Starita et al., 2018
Replicates showing depletion

Bouwman et al., 2013
Mutation type
AlignGVGD
Predicted splice effect
Literature predictions
Growth
IC50
Classification

Splicing Analysis

Walker et al., 2013
Author
Year
PubMed ID
Splicing aberration
Splicing aberration type
Functional assay performed

Houdayer et al., 2012
Methods
Assay report
Splicing classification

Wai et al., 2020
Variant position
Splicing results
RNA-seq result
Site of splice aberration

Wessex Clinical Genetics Service
Specimen
Splice abnormality
Sample type

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