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Variant Scientist Jobs in Boston, MA (NOW HIRING)

Ampersand

Senior Scientist I, Microfluidics

Boston, MA · On-site

$126 - $159.50/hr

  • Medical

  • Retirement

The Role Ampersand Biomedicines is seeking a Senior Scientist I to help build and apply cell-based, high-throughput capabilities for engineered antibody and protein variant library screening. This ...

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Broad Institute

Clinical Genomics Coordinator

Cambridge, MA · On-site

$58K - $76K/yr

  • Medical

  • Dental

  • Vision

  • Life

  • Retirement

  • PTO

Classify variant- and gene-disease associations * Support research projects that require curation ... BA or BS degree in the sciences with 2+ years as a Clinical Genomics Assistant or related ...

Novartis

Human Genetics Laboratory Leader

Cambridge, MA · On-site

$152K - $283K/yr

  • Medical

  • Life

  • Retirement

  • PTO

... variant genetics, functional biology, and advanced analytical approaches to inform target prioritization. This position is part of the Human Genetics & Targets group within the Discovery Sciences ...

Waters Corporation

Senior SAP VC AVC Modeler

Milford, MA · On-site

... variant configuration models in SAP S/4HANA that enable accurate product quoting in SAP CPQ. This ... Bachelor's degree in Engineering, Computer Science, Information Systems, or related field. * 5+ ...

Prattwhitney

SPY-6(V)4 Chief Engineer (CE)

Sudbury, MA · On-site

$157 - $299/hr

  • Medical

  • Dental

  • Vision

  • Life

  • Retirement

  • PTO

Together, we push the boundaries of known science and find new ways to connect and protect our ... This (V)4 variant is part of the SPY‑6 Family of Radars (FoRs) being produced by Raytheon on the ...

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All JobsVariant Scientist JobsVariant Scientist Jobs in Boston, MA

Variant Scientist information

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How much do variant scientist jobs pay per hour?

As of Aug 20, 2026, the average hourly pay for variant scientist in Boston, MA is $50.37, according to ZipRecruiter salary data. Most workers in this role earn between $36.54 and $63.82 per hour, depending on experience, location, and employer.

What is a variant scientist?

Variant Scientists are professionals who analyze genetic variants—differences in DNA sequences—to determine their significance in health and disease. They interpret genomic data, often from whole-genome or exome sequencing, to assess whether specific variants may cause or contribute to medical conditions. Their work is crucial in clinical genetics, precision medicine, and biomedical research, helping guide patient diagnosis and treatment. Variant Scientists collaborate with clinicians, bioinformaticians, and laboratory personnel to provide accurate and actionable genetic insights.

What does a variant scientist do?

As a variant scientist, you work for a research laboratory in a university or a medical facility to test and study variations of genes and the effects they have on human development. As part of your duties, you aid in the development of new tests to discover gene abnormalities, perform analysis on patient samples to identify possible mutations, and record your findings to assist in scientific research. You also have heavy reporting responsibilities that may require in-depth computer and writing skills, the ability to analyze data, and strong attention to detail. In this role, you may cater to a specific health field, like pediatrics or oncology.

What are the key skills and qualifications needed to thrive as a variant scientist, and why are they important?

To thrive as a Variant Scientist, you need a solid background in genetics, molecular biology, and bioinformatics, typically supported by an advanced degree such as a PhD or MSc in a related field. Familiarity with next-generation sequencing (NGS) platforms, variant annotation tools, and data analysis software like GATK or ANNOVAR is essential. Strong analytical thinking, attention to detail, and effective communication skills help you interpret complex genetic data and collaborate with multidisciplinary teams. These skills ensure accurate variant interpretation, drive discoveries, and support precision medicine initiatives.

What are some common challenges faced by variant scientists in interpreting genetic data, and how are these typically addressed within a team?

Variant Scientists often encounter challenges such as distinguishing between benign and pathogenic variants, managing large volumes of sequencing data, and staying updated with rapidly evolving genetic databases. These challenges are typically addressed by collaborating closely with bioinformaticians, clinical geneticists, and laboratory personnel to review findings and validate interpretations. Regular team meetings, use of standardized classification guidelines like ACMG, and leveraging advanced software tools help ensure accurate and consistent variant analysis.
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What are the most commonly searched types of Variant Scientist jobs in Boston, MA?

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For Variant Scientist jobs in Boston, MA, the most frequently searched job titles are:

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Variant Scientist jobs near you
Infographic showing various Variant Scientist job openings in Boston, MA as of August 2026, with employment types broken down into 100% Full Time. Highlights an 100% In-person job distribution, with an average salary of $104,768 per year, or $50.4 per hour.

Associate Director, Bioinformatics

Rhythm Pharmaceuticals

Boston, MA • On-site

Full-time

Re-posted 5 days ago

Job description

Company Overview
Rhythm is a global, commercial-stage biopharmaceutical company committed to transforming the lives of patients living with rare neuroendocrine diseases. We develop medicines for previously untreatable or undertreated diseases. We recognize the courage it takes for patients and their caregivers to begin their journey of advocacy to find the answers they need. Their courage inspires us to challenge convention, ask bold questions and seek answers for them. Every day, we strive for excellence through our willingness to adapt, learn, and our tenacity to overcome barriers, together.
Opportunity Overview
We are seeking a highly motivated Associate Director of Data Science within Rhythm's Research group and the Data Sciences Team in support of our clinical, regulatory, and scientific objectives in the rare neuroendocrine/obesity/metabolic disease. The successful candidate will have a strong background in biostatistics, genetics, and data analytics, and will be responsible for implementing advanced AI data models, predictive tools, and integrative analyses across the obesity and metabolic disease therapeutic areas. A core focus of this position will be the development and implementation of algorithmic phenotyping approaches using electronic medical records (EMR) and real-world datasets, enabling robust patient stratification, cohort definition, and integration with genomics and biomarker data. This position is ideal for a technically strong investigator who thrives in a fast-paced environment and is motivated to apply and scale high-impact data science infrastructure alongside a growing team.
Responsibilities and Duties
  • Design and deploy AI-driven, agent-based phenotyping pipelines that leverage EMR/EHR and real-world data to define disease cohorts, endpoints, and longitudinal outcomes.
  • Develop scalable approaches for cohort identification, feature extraction, and phenotype validation, including rule-based and machine learning methods.
  • Maintain high-throughput rare variant curation and classification models.
  • Execute the design, development, and deployment of data analysis pipelines, statistical models, and predictive tools to support Genetics-led programs.
  • Lead hands-on integration of clinical, EMR, genomics, and biomarker datasets, enabling multi-modal analyses.
  • Build and maintain reproducible workflows for data ingestion, harmonization (e.g., coding systems, ontologies), QC, and analysis (SQL, Python, R).
  • Apply statistical genetics and advanced analytics to link phenotypic definitions with genetic signals, including rare variant analyses.
  • Drive improvements in data infrastructure and phenotyping frameworks to support team expansion and increased dataset complexity.

Qualifications and Skills
  • Ph.D. in Biostatistics, Computational Biology, Genetics, Data Science, or related quantitative field.
  • ~5+ years of relevant experience in biotechnology, pharmaceuticals, or healthcare analytics.
  • Experience with neuroendocrine, obesity/metabolic-related biology and datasets.
  • Experience applying machine learning and AI models to real-world and clinical datasets, including model development, evaluation, and deployment in production or near-production settings.
  • Experience developing or utilizing AI-driven agents/workflows to automate data extraction, phenotyping, analysis, or knowledge generation tasks.
  • Strong hands-on expertise in SQL, Python, and R, with experience building production-quality data pipelines.
  • Experience with cloud computing and storage environments including AWS, GCP, Snowflake.
  • Demonstrated experience with variant calling pipelines, variant interpretation and ACMG rare variant classification.
  • Demonstrated experience in EMR/EHR and real-world data analysis (e.g., UK Biobank, All of Us) including cohort building and longitudinal data modeling.
  • Proven track record in algorithmic phenotyping, including use of coding systems (ICD, CPT, SNOMED), clinical ontologies, and feature engineering.
  • Familiarity with broader bioinformatics/multi-omics methodologies including RNA-seq, methylation analysis, long-read sequencing would be advantageous.
  • Strong problem-solving skills and ability to operate independently in a fast-paced, execution-focused environment.
  • Excellent communication skills with the ability to clearly present complex analytical outputs to technical stakeholders.

This role can be remote or based out of our corporate office in Boston, Massachusetts. Rhythm operates in a hybrid-work model. Candidates applying must be willing and able to be in the Boston office in coordination with their department and business needs. This role may involve some travel.
More about Rhythm
We are a dynamic and growing global team spanning more than a dozen countries. At Rhythm we are dedicated to transforming the lives of patients living with rare neuroendocrine diseases by rapidly advancing care and precision medicines that address the root cause. Our team is passionate about expanding access to reach more patients and developing novel therapies for other rare neuroendocrine diseases, including congenital hyperinsulinism. 
At Rhythm our core values are:
  • We are committed to advancing scientific understanding to improve patients’ lives
  • We are inspired to tackle tough challenges and have the courage to ask bold questions
  • We are eager to learn and adapt
  • We believe collaboration and ownership are foundational for our success
  • We value the unique contribution each individual brings to furthering our mission

Inherent in our core values is the commitment to act ethically and with integrity in all we do.
Rhythm is an equal employment opportunity employer and does not discriminate against any applicant because of race, creed, color, age, national origin, ancestry, religion, gender, sexual orientation, disability, genetic information, veteran status, military status, application for military service, or any other class protected by state or federal law.
Headquartered in Boston, Rhythm is proud to have been named one of the Top Places to Work in Massachusetts.
 

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