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Here is a plain-language breakdown of this genetic report:
🧬 Report Summary - Trio Whole Exome Sequencing
Lab: SN Gene Lab Pvt Ltd | Referred by: Dr. Sumitra Bachani, Safdarjung Hospital, Delhi
Samples tested: Fetus (AF of Priya Verma), Father (Mr. Mohit), Mother (Mrs. Priya Verma)
Test: Trio Whole Exome Analysis on Illumina NovaSeq 6000
👨👩👧 Who Was Tested
| Person | Sample ID | Details |
|---|---|---|
| Fetus (AF of Priya Verma) | 2400167082 | Sex not disclosed (per PC-PNDT Act) |
| Father (Mr. Mohit) | 2400167081 | Male |
| Mother (Mrs. Priya Verma) | 2400167080 | Female, 32 years |
🔵 FINDING 1 - MTHFR Gene Variants (The Original Reason for Testing)
Result: NEGATIVE - No concern, prenatal decisions cannot be based on this
The family was tested because:
- Mother (Mrs. Priya) has one copy of the MTHFR variant A1298C (heterozygous)
- Father (Mr. Mohit) has two copies of the MTHFR variant C677T (homozygous)
What was found in the fetus:
- The fetus has one copy of C677T (from father) AND one copy of A1298C (from mother) - this is called "compound heterozygous"
Key conclusion: Both MTHFR variants (C677T and A1298C) are classified as benign - meaning they do NOT cause disease. Prenatal decisions (like termination or intervention) cannot and should not be based on these MTHFR variants. This is an important reassurance.
🔴 FINDING 2 - GJB2 Gene Variant (Unexpected but Critical Finding)
Result: SIGNIFICANT - The fetus is affected with hereditary deafness
This is the most important part of the report. While checking the whole exome, a serious variant was found in the GJB2 gene (also known as Connexin-26), which causes non-syndromic sensorineural hearing loss (deafness).
| Finding | Fetus | Father (Mr. Mohit) | Mother (Mrs. Priya) |
|---|---|---|---|
| Gene | GJB2 | GJB2 | GJB2 |
| Variant | c.71G>A (p.Trp24Ter) | c.71G>A (p.Trp24Ter) | c.71G>A (p.Trp24Ter) |
| Copies affected | Both copies (Homozygous) | One copy (Heterozygous) | One copy (Heterozygous) |
| Status | AFFECTED (Pathogenic) | Carrier (no symptoms) | Carrier (no symptoms) |
| Inheritance | Autosomal Recessive | Autosomal Recessive | Autosomal Recessive |
What this means in simple terms:
- Both parents are silent carriers - they each carry one faulty copy of the GJB2 gene but have normal hearing themselves.
- The fetus inherited the faulty copy from BOTH parents, making it homozygous - meaning the fetus has two faulty copies.
- This means the fetus is expected to have congenital (from birth) sensorineural hearing loss (deafness) - condition called DFNB1A.
- Sensorineural deafness means the inner ear's nerve receptors or the auditory nerve pathway is affected. It is typically permanent.
Why this matters - The 1-in-4 Chance Rule:
When both parents are carriers of an autosomal recessive condition, each pregnancy has:
- 25% chance the child is affected (like this fetus)
- 50% chance the child is a carrier (like the parents)
- 25% chance the child is completely unaffected
📋 What the Lab Recommends
- Sanger sequencing to confirm this variant independently (standard practice to verify NGS findings).
- Genetic counseling - the family should meet a genetic counselor to fully understand implications.
- Family testing - other family members may want to be tested to know if they are also carriers.
- Annual re-review - gene interpretation can change as science advances.
⚙️ Technical Quality of the Test
The sequencing quality was excellent across all three samples:
| Metric | Fetus | Father | Mother |
|---|---|---|---|
| Data generated | 10.9 Gb | 6.51 Gb | 7.80 Gb |
| Reads aligned | 99.69% | 99.65% | 99.65% |
| High quality data (Q30) | 93.3% | 92.75% | 93.1% |
All values are well above acceptable thresholds - results are reliable.
🧾 Bottom Line
| Summary | |
|---|---|
| MTHFR finding | Benign - not a concern, no action needed |
| GJB2 finding | CRITICAL - The fetus is homozygous for a pathogenic variant. Congenital sensorineural deafness is expected. Both parents are silent carriers. |
| Next step | Genetic counseling is strongly advised before any decision. Confirmatory Sanger sequencing is recommended. |
Important note: This report was prepared prenatally (fetal DNA from amniotic fluid / CVS). The sex of the fetus was intentionally not disclosed as per India's PC-PNDT Act.
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