Carrier screening has outgrown the language we still use to explain it. The rapid expansion of genetic testing has uncovered new layers of complexity in how conditions present, how results should be interpreted, and how patients experience and act on genetic information. To practice responsibly in this era of Genetic Carrier Screening 3.0, clinicians must understand not only what we are testing for, but how and why the results look different than they did even five years ago. As testing panels grow, I am increasingly reminded that our challenge is no longer the technology; it is interpretation and communication. Patients deserve clarity, context, and thoughtful guidance that matches the complexity of the science we are placing in their hands.

Understanding genetic carrier screening 3.0

Carrier screening began as ethnicity-based testing. It then evolved into pan-ethnic panels such as the ACMG Tier 3 panel of 113 genes, promoting greater equity. But we are now living in the third era (Genetic Carrier Screening 3.0) defined by:

• More complex variant interpretation
• Clinical consequences for some “carriers” themselves
• Hidden carrier states even with “negative” results
• Hundreds of genes on expanded panels, not all clinically actionable

To illustrate how this impacts real-world clinical care, we begin with a gene most people think they already understand: CFTR.

CFTR: when being a “carrier” still has clinical meaning

The CFTR gene, classically associated with cystic fibrosis (CF), provides one of the clearest examples of why binary thinking about carrier status no longer works. Many of us learned that a person with one non-working CFTR gene is just a carrier; unaffected themselves, but capable of passing the condition on to offspring. Today, we know that is not always true. Certain CFTR variants can cause CFTR-related disorders even in individuals with just one altered copy. One of the most recognized manifestations is Congenital Bilateral Absence of the Vas Deferens (CBAVD), a form of obstructive male infertility. These men typically have normal lung and pancreatic function and no family history of CF. The difference often lies in a specific CFTR variant called the 5T allele, and the number of adjacent TG repeats.

What is the 5T allele

The 5T allele occurs in a region of intron 8 of the CFTR gene called the poly-T tract, which normally contains 7 or 9 thymidine (T) nucleotides. Some individuals have only 5 Ts, and this shorter sequence interferes with proper splicing of exon 9 during mRNA processing, resulting in a reduction in functional CFTR protein.

• 9T: Normal; no functional concern.
• 7T: Mildly reduces CFTR protein production.
• 5T: Significantly reduces CFTR protein production.

Because it reduces protein output, the 5T allele is considered a variable-expressivity mutation; it may not cause classic cystic fibrosis, but it can contribute to CFTR-related disorders, including:

• Congenital bilateral absence of the vas deferens (CBAVD) → male infertility
• Chronic sinus or lung issues
• Mild or atypical CF presentations

What are TG repeats and why do they matter

Immediately adjacent to the poly-T tract is a sequence of TG repeats, which can contain 11, 12, or 13 TG units. The number of TG repeats modifies the severity of the 5T allele. The longer the TG sequence, the more it disrupts normal CFTR function.

• TG11-5T: Mild effect.
• TG12-5T: Moderate effect.
• TG13-5T: Highest effect; greatest risk of CFTR-related disease.

Key takeaway: A 5T result is meaningless without knowing the TG repeat number.

Why this matters in carrier screening

The 5T allele on its own may not signal a clinically meaningful risk, but its effect depends on:

• The number of TG repeats next to it, and
• What variant (if any) is present on the other CFTR gene

For example:

• A man with TG13-5T / normal CFTR has a high likelihood of CBAVD and subsequent infertility.
• If a person has 5T on one CFTR gene and a second CFTR mutation on the other, the likelihood of disease (in themselves or in their children) significantly increases.

Key takeaway: Not all CFTR “carriers” are asymptomatic; some have clinically relevant disease. When one reproductive partner carries a CFTR variant, the other partner’s test must include full CFTR sequencing with poly-T/TG tract analysis to accurately assess reproductive risk. Even if that partner’s result is “negative,” residual risk remains, because no carrier screen detects 100 percent of possible CFTR variants.

Key takeaway: Full CFTR sequencing, not basic screening, is required to properly assess risk when a 5T/TG variant is present.

Visual: CFTR 5T/TG tract and clinical impact

• TG11 + 5T → Low likelihood of symptoms
• TG12 + 5T → Moderate likelihood of CBAVD
• TG13 + 5T → High likelihood of CBAVD or CF-related disorder

A simple analogy for patients

Think of the CFTR gene like a factory assembly line that produces a vital product:

• 9T: Fully staffed shift (normal production).
• 7T: Short-staffed; fewer products made.
• 5T: Severely understaffed; low product output.

Now add workplace pressure as the TG repeats:

• TG11: Mild pressure.
• TG12: Moderate pressure.
• TG13: Extreme pressure.

So 5T + TG13 is like having too few workers under intense pressure; the lowest output and highest chance of clinical impact.

SMA: the silent carrier challenge

Another powerful example of modern carrier screening complexity is Spinal Muscular Atrophy (SMA). SMA is caused by pathogenic variants in the SMN1 gene. Traditional screening measures how many copies of SMN1 a person has. Most individuals have two copies total; one on each chromosome (1 + 1).

However, a person can still be a carrier even if two copies are detected. This happens when both copies sit on the same chromosome and none on the other; a configuration called 2+0. Because standard testing only counts total copies, these individuals appear “negative” despite being true carriers. We now refer to them as silent carriers.

• Normal: [ SMN1 ] + [ SMN1 ] → 2 copies (1 + 1) Not a carrier.
• Carrier: [ SMN1 ] + [ – ] → 1 copy (1 + 0) Carrier.
• Silent: [ SMN1 | SMN1 ] + [ – ] → 2 copies (2 + 0) Still a carrier.

A linked marker, SMN1 g.27134T>G (also written *c.*3+80T>G), increases the likelihood that a person with two SMN1 copies actually carries them in the 2+0 arrangement. The significance of this marker varies by ancestry.

Key takeaway: A “2-copy” SMA result is not always reassuring; evaluate whether the silent carrier marker is present. If one partner is a known carrier and the other has two SMN1 copies plus this risk marker, prenatal diagnostic testing (CVS or amniocentesis) should be discussed to directly assess fetal status. This protects families from false reassurance and supports informed decision-making.

Hemoglobinopathies: When “traits” are not silent

Hemoglobinopathies provide another important lesson: being a “carrier” does not always mean being clinically unaffected. In β-thalassemia, what is missing is reduced or absent β-globin chain production due to mutations in the HBB gene. Depending on the degree of β-globin loss, clinical presentation varies along a spectrum:

• β-thalassemia minor (trait): Mild reduction of β-globin leading to microcytosis with or without mild anemia; often misdiagnosed as iron deficiency, resulting in unnecessary iron therapy.
• β-thalassemia intermedia: Moderate reduction in β-globin with moderate anemia.
• β-thalassemia major (Cooley’s anemia): Severe or absent β-globin production, causing profound anemia requiring lifelong transfusions.

In α-thalassemia, what is missing is one or more of the four α-globin genes (two on each chromosome 16). Clinical expression correlates directly with the number of α-gene deletions:

• 1 (–α/αα): Silent carrier. No symptoms.
• 2 (–α/–α or ––/αα): α-thalassemia trait. Mild microcytosis ± mild anemia.
• 3 (––/–α): Hemoglobin H disease. Moderate-severe hemolytic anemia due to HbH (β₄) formation.
• 4 (––/––): Hydrops fetalis with Hb Bart’s. Incompatible with life (unless treated in utero) due to Hb Bart’s (γ₄).

Even Sickle Cell Trait (SCT), long described as benign, can have clinical consequences. Individuals with SCT may have increased risks of renal papillary necrosis, venous thromboembolism, and, in rare cases, exercise-related collapse under extreme exertion or dehydration.

Key takeaway: Hemoglobinopathy “traits” are not always silent. They may carry health implications of their own; not just reproductive implications. Because ethnic-based screening missed many carriers, the American College of Obstetricians and Gynecologists (ACOG) now recommends universal hemoglobinopathy testing for all individuals planning pregnancy or currently pregnant, regardless of race or ancestry.

X-linked conditions: Carrier status affects mothers too

X-linked conditions illustrate another essential point: carrier status can affect maternal health, not just fetal outcomes. Including conditions such as Duchenne Muscular Dystrophy, Hemophilia, VWD, and G6PD deficiency widens the relevance of carrier screening across diverse populations, reinforces that carriers are not always clinically unaffected, and highlights key implications for pregnancy safety and counseling. In Duchenne Muscular Dystrophy (DMD), approximately 8 percent of female carriers develop cardiomyopathy. Baseline cardiac evaluation, and ongoing monitoring during and after pregnancy, is recommended. Women who carry hemophilia A/B or von Willebrand Disease (VWD) variants may have reduced clotting factor levels, increasing bleeding risk during childbirth and postpartum recovery. The American Society of Hematology (ASH) advises proactive factor level monitoring, multidisciplinary delivery planning, and postpartum management for these carriers. Female carriers of G6D deficiency (a common X-linked condition with high prevalence in African, Mediterranean, Middle Eastern, and Asian populations) may experience episodic hemolysis triggered by infections, certain medications (e.g., sulfonamides, nitrofurantoin), or fava bean ingestion. Due to X-inactivation (lyonization), carriers can be clinically affected, particularly during pregnancy when oxidative stress is heightened. This underscores the need for maternal counseling, medication safety review, and culturally relevant dietary guidance.

Key takeaway: X-linked carrier screening is not only about fetal risk; it informs maternal safety, pregnancy care, and equitable counseling across diverse patient populations.

Oluyemisi (Yemi) Famuyiwa is a renowned fertility specialist and founder, Montgomery Fertility Center, committed to guiding individuals and couples on their path to parenthood with personalized care. With a background in obstetrics and gynecology from Georgetown University Hospital and reproductive endocrinology and infertility from the National Institutes of Health, she offers cutting-edge treatments like IVF and genetic testing. She can be reached on Linktr.ee, LinkedIn, YouTube, Facebook, Instagram @montgomeryfertility, and X @MontgomeryF_C.