Tag: ClinVar

Datasets | TogoVar

Variant frequencies for which you can apply for use of individual-level data∗1 to the NBDC human databases∗2 Click the links at the Included controlled-access datasets to apply for use of individual-level data ∗1:fastq/bam/cel files and/or lists of genotype data etc.∗2:Japanese Genotype-phenotype Archive (JGA) / AMED Genome group sharing Database (AGD)…

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FarGen Phase One Sequences Exomes of Nearly 500 From Faroe Islands

Researchers have sequenced the exomes of 473 individuals as part of the first phase of the Faroe Genome Project (FarGen), which aims to develop a reference catalog for the isolated archipelago nation. As the researchers report in the European Journal of Human Genetics, the FarGen cohort includes more than 1,500…

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Myriad Genetics to Submit Hereditary Cancer Risk Variants to ClinVar in 2023

NEW YORK – Myriad Genetics will begin submitting variants detected by its hereditary cancer risk test, including variants in BRCA1 and BRCA2 genes, to the public database ClinVar starting in the spring of 2023. The Salt Lake City-based company is infamous, derided, and even boycotted in certain circles in the…

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Webinar: Mastermind’s New ClinVar Integration

ABOUT THE WEBINARClinVar is a public archive of information submitted by genetic testing labs on the relationships between medically important genetic variants and their clinical characteristics found in patients. Now, all published variants, pathogenicity interpretations, and other key information within ClinVar’s database are included as part of Mastermind’s comprehensive body…

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NM_005445.4(SMC3):c.181C>T (p.Arg61Trp) AND Cornelia de Lange syndrome 3 – ClinVar

NM_005445.4(SMC3):c.181C>T (p.Arg61Trp) AND Cornelia de Lange syndrome 3 Based on: 1 submission [Details] Record status: current Accession: RCV000760292.1 Allele description [Variation Report for NM_005445.4(SMC3):c.181C>T (p.Arg61Trp)] NM_005445.4(SMC3):c.181C>T (p.Arg61Trp) Gene: SMC3:structural maintenance of chromosomes 3 [Gene – OMIM – HGNC] Variant type: single nucleotide variant Cytogenetic location: 10q25.2 Genomic location: Preferred name:…

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NM_005359.6(SMAD4):c.1630C>A (p.Pro544Thr) AND Hereditary cancer-predisposing syndrome – ClinVar

NM_005359.6(SMAD4):c.1630C>A (p.Pro544Thr) AND Hereditary cancer-predisposing syndrome Based on: 1 submission [Details] Record status: current Accession: RCV001012497.1 Allele description [Variation Report for NM_005359.6(SMAD4):c.1630C>A (p.Pro544Thr)] NM_005359.6(SMAD4):c.1630C>A (p.Pro544Thr) Gene: SMAD4:SMAD family member 4 [Gene – OMIM – HGNC] Variant type: single nucleotide variant Cytogenetic location: 18q21.2 Genomic location: Preferred name: NM_005359.6(SMAD4):c.1630C>A (p.Pro544Thr) HGVS:…

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Job – Principal Biostistician/Bioinformatics job at Kenya Medical Research

Vacancy title: Principal Biostistician/Bioinformatics [ Type: FULL TIME , Industry: Research , Category: Research ] Jobs at: Kenya Medical Research – KEMRI Deadline of this Job: 06 October 2022   Duty Station: Within Kenya , Kisumu , East Africa SummaryDate Posted: Tuesday, September 20, 2022 , Base Salary: Not Disclosed…

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Human hg38 chr7:73,678,750-73,740,129 UCSC Genome Browser v435

Use drop-down controls below and press refresh to alter tracks displayed.Tracks with lots of items will automatically be displayed in more compact modes.    Custom Tracks H3K27ac Meta NeuN SCZhidedensesquishpackfull H3K27ac NeuN SCZ del_CRDhidedensesquishpackfull H3K27ac NeuN SCZ del_CRD_del_peakshidedensesquishpackfull H3K27ac Tissuehidedensesquishpackfull H3K27ac Tissue BDhidedensesquishpackfull H3K27ac Tissue BD del_CRDhidedensesquishpackfull H3K27ac Tissue BD…

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List of variants in gene CEP19 reported as benign

List of variants in gene CEP19 reported as benign – ClinVar Miner The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website….

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iPSCs derived from infertile men carrying complex genetic abnormalities can generate primordial germ-like cells

Patients and controls The patient 1 was 38 years old and consulted for infertility after he and his partner had been trying to conceive for 2 years. The patient was the first child of unrelated parents, and he had four brothers and five sisters whose fertility status could not be determined…

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The number of unique SNPs and indels in Clinvar

The number of unique SNPs and indels in Clinvar 1 Is it provided by clinvar or an easy way to get the number of unique SNPs and indels in Clinvar? I have found the unique variation record in here. But this also included structural variation such as CNVs. ClinVar submissions…

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python – Matching two files(vcf to maf) using a dictionaries, and appending the contents

annotation_file ##INFO=<ID=ClinVar_CLNSIG,Number=.,xxx ##INFO=<ID=ClinVar_CLNREVSTAT,Number=.,yyy ##INFO=<ID=ClinVar_CLNDN,Number=.zzz #CHROM POS ID REF ALT QUAL FILTER INFO chr1 10145 . AAC A 101.83 . AC=2;AF=0.067;AN=30;aaa chr1 10146 . AC A 98.25 . AC=2;AF=0.083;AN=24;bbb chr1 10146 . AC * 79.25 . AC=2;AF=0.083;AN=24;ccc chr1 10439 . AC A 81.33 . AC=1;AF=0.008333;AN=120;ddd chr1 10450 . T G 53.09…

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Annotating with CADD, gnomad, Clinvar & dbNSFP on UKB RAP – Feature Requests

dint May 9, 2022, 1:33pm #1 i’m just wondering if you can specify cadd, gnomad, clinvar and dbNSFP options when annotating with hail on dxjupyterlab_spark_cluster o the UKB RAP? From the hail website, the following command can be used on your matrix file to annotate with these features: db =…

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VCV000038126.28 Observations – ClinVar – NCBI

1 SCV000301220.2 Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) Pathogenic reviewed by expert panel curation Breast-ovarian cancer, familial, susceptibility to, 2 (unknown ) germline Variant allele predicted to encode a truncated non-functional protein. 1 SCV000785901.2 Counsyl Pathogenic criteria provided,single submitter clinical testing Breast-ovarian cancer, familial, susceptibility to,…

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Penetrance of Mendelian Disease Variants Ranges in Heterozygous Carriers

NEW YORK – Using genetic data from the UK Biobank, a team from Brigham and Women’s Hospital, the Broad Institute, Harvard Medical School, and the Massachusetts Institute of Technology has documented various levels of recessiveness for variants previously implicated in Mendelian conditions. “With increasing exome sequencing of population biobank cohorts,…

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BAM file and no RNAME or POS information? : bioinformatics

Newbie here. Please, play nice. I got possession of a set of 4 .bam files that stores the exome of an individual, around 400 MB each. I used samtools to generate a 2.4 GB .sam file out of one of the .bam files, and I found it contains lines with…

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Genetic and chemotherapeutic influences on germline hypermutation

DNM filtering in 100,000 Genomes Project We analysed DNMs called in 13,949 parent–offspring trios from 12,609 families from the rare disease programme of the 100,000 Genomes Project. The rare disease cohort includes individuals with a wide array of diseases, including neurodevelopmental disorders, cardiovascular disorders, renal and urinary tract disorders, ophthalmological…

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Mining Curated Databases for Literature in VSClinical

Curated databases are a real-time saver when compiling published evidence to support your variant evaluations and classifications. Leveraging the curated databases at your fingertips in our VSClinical variant interpretation hub is even more efficient. Not only does VSClinical provides users with automated variant classification for germline variants according to the…

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Bioinformatics Data Engineer in Boston, MA for Dana-Farber Cancer Institute

Details Posted: 27-Apr-22 Location: Boston, Massachusetts Salary: Open Categories: Staff/Administrative Internal Number: 2022-26005 Located in Boston and the surrounding communities, Dana-Farber Cancer Institute (DFCI) brings together world renowned clinicians, innovative researchers and dedicated professionals, allies in the common mission of conquering cancer, HIV/AIDS and related diseases. Combining extremely talented people…

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Bioinformatics Analyst II – Remote in Danville, PA for Geisinger

Details Posted: 22-Apr-22 Location: Danville, Pennsylvania Type: Full Time Salary: Open Categories: Operations Job Summary Primary accountability is to leverage the organization’s data assets exome sequencing data (>180,000 individuals) from MyCode Community Health Initiative to improve quality, efficiency and generate knowledge specifically in the field of bioinformatics within health research….

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VCV001049045.1 – ClinVar – NCBI

The TBP p.Gln87_Gln95del variant was not identified in the literature nor was it identified in dbSNP, ClinVar, Cosmic or LOVD 3.0. The variant was also not identified in the following control databases: the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project, the Exome Aggregation Consortium (August 8th 2016), or…

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VCV000866285.4 – ClinVar – NCBI

Likely pathogenic (Feb 04, 2019) criteria provided, single submitter Method: clinical testing Retinal dystrophy Affected status: yes Allele origin: germline Blueprint Genetics Accession: SCV001239720.1 Submitted: (Oct 15, 2019) Comment: My Retina Tracker patient Likely benign (Dec 30, 2019) criteria provided, single submitter Method: clinical testing not provided Affected status: unknown…

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using ANNOVAR annotation clinvar database out wrong position

using ANNOVAR annotation clinvar database out wrong position 0 Hello Biostars, I was trying to annotate the VCF using ANNOVAR,but I get a wrong out ,it seems my clinvar database is not sutibale bcftools_callCommand=call -m -v -o /project/plantform/20220316PCR/03.amplify/L2107973CFD7G5kxT1/L2107973CFD7G5kxT1.variation.vcf /project/plantform/20220316PCR/03.amplify/L2107973CFD7G5kxT1/L2107973CFD7G5kxT1.mpileup.vcf clinvar ANNOVAR • 34 views Read more here: Source link

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VCV000698353.6 – ClinVar – NCBI

Likely benign (Nov 17, 2018) criteria provided, single submitter Method: clinical testing Arrhythmia Affected status: unknown Allele origin: germline Color Health, Inc Accession: SCV001358509.1 Submitted: (May 19, 2020) Likely benign (Apr 19, 2020) criteria provided, single submitter Method: clinical testing Long QT syndrome Affected status: unknown Allele origin: germline Invitae…

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rs532111960 RefSNP Report – dbSNP

Help Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When…

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rs9789283 RefSNP Report – dbSNP

Help Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When…

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VCV000977988.1 – ClinVar – NCBI

Pathogenic (May 10, 2019) criteria provided, single submitter Method: research Familial hypercholesterolemia 1 Affected status: yes Allele origin: germline Brunham Lab, Centre for Heart and Lung Innovation,University of British Columbia Accession: SCV001432616.1 Submitted: (Sep 16, 2020) Observation 1: Number of individuals with the variant: 1 Clinical Features: Dutch Lipid Clinic…

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VCV001120242.1 – ClinVar – NCBI

Likely pathogenic (Jun 01, 2021) criteria provided, single submitter (ACMG Guidelines, 2015) Method: research Postaxial polydactyly type A1 (Autosomal dominant inheritance) Affected status: yes Allele origin: germline Institute for Medical Genetics and Human Genetics, Charité – Universitätsmedizin Berlin Additional submitter: CUBI – Core Unit Bioinformatics,Berlin Institute of Health Accession: SCV001653577.1…

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Promethease report : promethease

Recently purchased a promethease report, and was surprised to find that a significant gene mutation was not included anywhere in the report. Subsequent search, found it had been rated a 0 in terms of magnitude – yet we know this is not the case. Does this report only include known…

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VCV000445854.7 Observations – ClinVar – NCBI

1 SCV000610624.1 Center for Pediatric Genomic Medicine,Children’s Mercy Hospital and Clinics Benign criteria provided,single submitter clinical testing not provided (not provided ) germline 1 SCV000700353.2 Eurofins NTD, LLC Uncertain significance criteria provided,single submitter clinical testing 1 not provided (unknown ) germline 1 Single Heterozygote www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CYP21A2 mixed 1 SCV001137083.1 Mendelics Benign…

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VCV001048762.1 – ClinVar – NCBI

Pathogenic (-) no assertion criteria provided Method: clinical testing Secondary hypothyroidism (Autosomal recessive inheritance) Allele origin: germline Department of Clinical Genetics and Genetic Counseling,Mediscan Systems Accession: SCV001548494.1 Submitted: (Apr 05, 2021) Evidence details Publications PubMed (1) Comment: The p.Ala37LeufsX38 mutation is not reported in the literature so far, however it…

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The structural coverage of the human proteome before and after AlphaFold

Abstract The protein structure field is experiencing a revolution. From the increased throughput of techniques to determine experimental structures, to developments such as cryo-EM that allow us to find the structures of large protein complexes or, more recently, the development of artificial intelligence tools, such as AlphaFold, that can predict…

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CRISPR-Based Therapeutics Blaze an In Vivo Path to the Clinic

Therapeutic applications of genome editing were envisioned at least as early as the mid-1990s, when the first sequence-specific genome editing technologies emerged. Initially, such applications were considered distant prospects, but by 2012, they suddenly seemed near to hand. It was at that time that CRISPR technologies emerged. CRISPR, which stands…

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Bioinformatics Analyst II in Danville, PA for Geisinger

Job Summary Primary accountability is to leverage the organization’s data assets exome sequencing data (>180,000 individuals) from MyCode Community Health Initiative to improve quality, efficiency and generate knowledge specifically in the field of bioinformatics within health research. Performs and supervises complex data extraction, transformation, visualization, and summarization to support Research…

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