Medical Oncologist
CION Cancer Clinics
RNA sequencing: resolving an uncertain splice-site change | CION Cancer Clinics
Standard genetic testing reads DNA, the master copy in every cell. RNA sequencing reads the working copies the cell actually builds from it, which is the only way to tell whether a change near a splice junction genuinely disrupted the gene. This page explains when this follow-up test is used, what it involves, and what it cannot answer on its own. At CION Cancer Clinics in Hyderabad, our oncologists review your family history with you and guide you to the right genetic counselling and testing.
NG
Medically reviewed by Dr. Naresh GunduConsultant Medical Oncologist · MBBS, DNB (Internal Medicine), DM (Medical Oncology, AIIMS) · last reviewed September 2026, next review due September 2027
17+specialists on panel
15,000+patients treated
35+centres across Telangana & AP
4.8★ / 800+Google rating
On this page
- What does RNA sequencing add to a DNA result?
- In which situations does a team ask for RNA sequencing?
- What actually happens during RNA testing?
- Words an RNA report uses
- DNA sequencing and RNA sequencing, compared
- What RNA sequencing cannot settle on its own
- What families get wrong about RNA testing
- Common questions about RNA sequencing
The short answer
What does RNA sequencing add to a DNA result?
Standard genetic testing reads DNA, the master copy stored in every cell. RNA sequencing reads the working copies the cell actually makes from that master copy before building a protein. For most spelling changes, the DNA reading is enough. For a change sitting near a splicing junction, it often is not.
Why splicing matters here
Genes are stored in sections, and the cell stitches the useful sections together while cutting the rest out. That stitching process is called splicing. A DNA change near one of these joins can look harmless on paper, yet still cause the cell to stitch the gene together wrongly.
Why DNA alone cannot always tell
Prediction tools can guess whether a change near a splice junction is likely to cause trouble, but a guess is not proof. RNA sequencing checks what the cell actually produced, which turns a prediction into an observation. It is ordered when a DNA finding is suspicious but not settled, and it is usually the deciding piece of evidence rather than the starting point of the investigation.
RNA sequencing answers "what did the cell do with this change", not "is this change dangerous in general".When it gets ordered
In which situations does a team ask for RNA sequencing?
This is a follow-up test in almost every case, added after a DNA result raises a specific question.
An uncertain change near a splice site
The DNA change sits close to the boundary between two gene sections. RNA sequencing shows whether that boundary was read correctly by the cell or not.
Reclassifying an older uncertain result
A change reported years ago as uncertain can sometimes be resolved now that RNA testing has become more widely available, without needing a fresh DNA sample.
Research and specialist referral centres
Not every laboratory offers this test routinely. It is more often arranged through a specialist genetics centre once a DNA finding needs a second layer of evidence.
Not a routine first test
Most people are never offered RNA sequencing, because most gene changes do not sit near a splice junction and DNA sequencing settles the question on its own.
Not sure whether this applies to you?
Ask an oncologistHow the sample is handled
What actually happens during RNA testing?
A fresh sample is collected
RNA breaks down quickly, so a special blood tube, or occasionally a tissue sample, is used and sent to the laboratory without delay.
The working copies are extracted
The laboratory isolates the RNA copies the cell was actively using from that gene at the time the sample was taken.
The copies are read and compared
Those copies are sequenced and lined up against the expected, correctly stitched version of the gene to spot any difference.
A geneticist interprets the pattern
A specialist decides whether the stitching pattern seen explains the original DNA finding, and writes that conclusion into your report.
On your report
Words an RNA report uses
- Splicing
- The process of cutting out unneeded sections of a gene's working copy and joining the useful sections together.
- Splice site
- The exact boundary where one gene section ends and cutting or joining happens. A change here can disrupt the whole process.
- Exon
- A section of a gene that is normally kept in the final working copy.
- Exon skipping
- A section that should have been kept is left out of the working copy entirely, which usually disrupts the protein made from it.
- Transcript
- Another word for the working copy of a gene that RNA sequencing reads directly.
- Aberrant splicing
- Stitching that has gone wrong, producing a working copy that does not match the correct version of the gene.
Leave a number, we will call you
One field. No form to fill in, and no charge for the call.
Side by side
DNA sequencing and RNA sequencing, compared
DNA sequencing
RNA sequencing
Reads the master copy stored in every cell
Reads the working copies the cell actually built
Can flag a splice-site change as suspicious
Can show whether that change actually disrupted splicing
Standard first test for inherited cancer risk
A follow-up test, used to resolve a specific DNA finding
Sample keeps well and travels easily
Sample is fragile and time-sensitive
Being straight with you
What RNA sequencing cannot settle on its own
RNA sequencing is powerful for the exact question it was designed for and unhelpful outside it. It cannot search broadly for faults the way a DNA panel does, and it is not the right first test for someone who has never had a DNA result at all.
It needs the right sample, at the right time
Splicing can differ between tissues and can change with how a cell is behaving at the moment of sampling. A result taken from blood does not always speak for how a gene behaves in the organ where the cancer arose, and your team will explain that limitation for your specific finding. This is one reason the test is arranged carefully rather than ordered as a routine add-on.
Who this does not apply to
If your report has come back with a clear pathogenic or clear benign result, RNA sequencing usually adds nothing. It is reserved for the narrower group whose DNA result is genuinely uncertain because of where the change sits.
If your report already uses the words "variant of uncertain significance" near a splice site, ask your counsellor whether RNA testing is available for your specific change.Commonly believed
What families get wrong about RNA testing
"RNA testing is more accurate than DNA testing, so I should ask for it instead."
They are not competing tests. DNA sequencing remains the standard first step. RNA testing answers one narrow follow-up question that DNA alone sometimes cannot.
"If a prediction tool says a change is harmless, that settles it."
Prediction tools estimate likelihood, they do not observe what happened. RNA sequencing is exactly how a prediction gets checked against reality.
"This test can be done anywhere with any blood sample."
RNA is fragile and time-sensitive, and not every laboratory offers this analysis. It is usually arranged through a specialist genetics centre with the right handling in place.
"A splicing problem always means the worst outcome."
Some disrupted splicing patterns still allow a partly working protein to be made. A geneticist weighs the specific pattern seen, not just the fact that splicing was affected.
Questions we are asked
Common questions about RNA sequencing
Is RNA testing done instead of DNA testing?
No. It is done after a DNA result to resolve a specific splice-site question. Almost everyone starts with DNA sequencing, and only a small number go on to need an RNA study.
Why does the sample need to arrive so quickly?
RNA breaks down faster than DNA once outside the body. Laboratories use special collection tubes and strict handling to keep the working copies intact until they can be read.
Can this test be repeated years after my original result?
Yes. RNA testing can often be arranged on a fresh sample well after the original DNA test, which is useful when an old uncertain result was never resolved.
Does every laboratory in India offer RNA sequencing?
No, it is offered by fewer centres than standard DNA panels. Your oncologist or counsellor can tell you where it is available and whether your situation needs it.
What if the RNA result still does not settle the question?
Occasionally the pattern seen is itself ambiguous. In that case the variant usually stays classified as uncertain, and your counsellor will explain what, if anything, is watched more closely as a result.
Does an abnormal splicing result change my treatment straight away?
Not on its own. The finding is reviewed alongside your family history and the rest of your report before any decision about treatment or surveillance is made.
Can my relatives be tested using RNA sequencing too?
Once a specific splicing effect is confirmed in one relative, other family members are usually tested with a simpler, targeted DNA test for that exact change rather than repeating the RNA study.
Where do I start if my report already mentions a splice-site change?
Take the report to a genetic counsellor and ask directly whether RNA testing is available for that change. Call the CION helpline if you are not sure who to approach next.
Your Specialists
Meet CION's oncologists. Bring your family history or genetic report to them.
Our medical oncologists see people with a strong family history of cancer, arrange genetic counselling and testing where it fits, and plan the checks that follow.
Medical Oncologist
Dr. C. Raghavendra Reddy
MBBS(Gold Medal), DNB(General Medicine), DM(Medical Oncology)(Gold Medal)
Medical Oncologist
Dr. Bharati Devi Gorantla
MBBS, MD(General Medicine), DM(Medical Oncology)(Adyar,Chennai), ECMO, MRCP SCE(UK)
Medical Oncologist
Dr. Owais Mohammed
MBBS, MD (General Medicine), DrNB (Medical Oncology), ECMO, MRCP SCE (Medical Oncology) (UK)
Medical Oncologist
Medical Oncologist
Want a specific doctor for your case? Mention them when booking.
Book Free ConsultationBook an appointment with our specialist
Share your name and number — we'll call you back within 30 minutes to schedule your consultation.
Sources
- MedlinePlus Genetics — How is genetic testing done?
- GeneReviews (NCBI Bookshelf) — GeneReviews: Medical Genetics Information Resource
- American College of Medical Genetics and Genomics — Standards and guidelines for the interpretation of sequence variants
- National Cancer Institute — Genetic Testing for Inherited Cancer Susceptibility Syndromes
This page is general information, not a prescription. Do not change or stop any treatment based on what you read here. If anything is worrying you, contact your own treating team — or call our helpline and we will help you reach the right specialist.
Keep reading
Related pages
'Variant of uncertain significance' in a germline reportThe result RNA sequencing is often used to resolveFunctional assays: testing what a variant actually doesAnother way an uncertain finding gets checked directlyWhole exome sequencing explainedThe broader DNA test this usually followsWhy two labs can classify the same variant differentlyWhy extra evidence like this can change a classification
Talk to us
Has your report flagged a splice-site change?
Tell us what your report says and we will explain, honestly, whether RNA testing is available and relevant for your situation. One helpline serves every CION centre.