Patient record

VP-10684

55-64 · Male · Family history of colorectal cancer

No material change

Current evidence agrees with the interpretation issued for this record.

Patient summary

Record: VP-10684
Age band: 55-64
Sex: Male
Test date: 24 Jan 2023
Reporting laboratory: Genomics Core Laboratory
Ordering department: Gastroenterology
Clinical owner: Dr. H. Nassar
Last contact: 14 Feb 2023
Indication: Family history of colorectal cancer

Synthetic record. No identifiers in this workspace correspond to a real person.

Historical finding

ClinVar

APCc.4399C>T (p.Pro1467Ser)

Panel: Gastrointestinal cancer panel
Condition: Familial adenomatous polyposis
ClinVar: VCV000411419
dbSNP: rs749142480
As reported: Benign
Reported on: 5 Sept 2022

Observed at appreciable population frequency. Reported as benign and excluded from the clinical summary.

Current interpretation

Read from ClinVar at the last evidence sync.

Classification: Benign
Consensus status: Reviewed by expert panel
Evidence confidence: Strong3 of 4 review criteria met
Last evaluated: 26 Feb 2023
Submissions: 11
Molecular consequence: missense variant
Variant type: single nucleotide variant
Location: chr5:112839993 (GRCh38)

Evidence summary

Decision support

Current evidence for APC c.4399C>T agrees with the benign interpretation issued in 2022. The classification was last evaluated on 26 Feb 2023 and carries 11 submissions.

Composed from the structured fields of the records cited on this page. Requires clinical verification before it informs any decision.

How VariantPulse reached this resultEight steps, each one inspectable

1Historical record retrievedAPC c.4399C>T reported as Benign on 2022-09-05.
2Variant normalisedResolved to ClinVar VCV000411419 (rs749142480) and keyed as APC:c.4399C>T.
3Current evidence retrievedRead live from ClinVar: Benign, 11 submissions, reviewed by expert panel.
4Classification difference detectedRecorded interpretation normalised to Benign. Current interpretation normalised to Benign. Codes are identical, so no reclassification has occurred.
5Regional sources comparedRegional index asserts Benign, consistent with the global reading.
6Impacted records identified12,482 findings checked; 4 carry this variant.
7Evidence brief generatedComposed from the structured fields of the cited records above.
8Human review requestedVariantPulse does not change any record. A clinician decides what happens next.

Global and regional evidence

Sources agree

Global

Benign

Submissions: 11
Review status: Reviewed by expert panel
Last evaluated: 26 Feb 2023
Reference frequency: 5.00e-5

Read from ClinVar, which aggregates submissions dominated by European-ancestry cohorts.

Regional

Benign

Observations: 87
Cohort size: 5,400
Last updated: 30 Jan 2026
Regional frequency: 1.61e-2

Modelled regional aggregation maintained inside this workspace.

VariantPulse analysis

Both sources place this variant in the same band, so there is no divergence to resolve. Common in both regional and global cohorts. Benign in both readings.

How the interpretation changed

APC c.4399C>T — the DNA is unchanged. The evidence around it is not.

2022Genetic test performedFirst record on file carrying APC c.4399C>T.
2022Reported as benignObserved at appreciable population frequency. Reported as benign and excluded from the clinical summary.
2023Submissions accumulated11 independent submissions now contribute to the classification.
TodayVariantPulse identified the affected records4 historical records carry this variant and were flagged for clinical review.

Decision support only. Final interpretation remains with the qualified clinical team.