About BRCA1
No gene-level summary was recorded for this case.
No variant summary was recorded for this case.
Five-step scale from benign to pathogenic. This variant is uncertain. Select a step to read what it means.
Uncertain.The recorded classification is uncertain significance.
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.No gene-level summary was recorded for this case.
The recorded framework is ClinGen BRCA1 VCEP v1.2.0. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
The applied criteria and their strengths are shown as assessed under the stated framework.
In a calibrated BRCA1 functional study, this variant showed loss of function similar to pathogenic control variants. The ENIGMA BRCA1/2 specification assigns PS3 at Strong strength for BRCA1 c.5200T>A (p.Phe1734Ile).
Expert panel ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen classified as Likely pathogenic.
No benign criterion marked as applied in the recorded assessment.
ENIGMA BRCA1 and BRCA2 Specification v1.2.0 final-classification framework (Table 3 criteria-combination rules).
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1 allele counts were not recorded for this variant.
Absent from gnomAD v2.1.
Recorded SpliceAI maximum delta score: 0.000. Refer to the recorded PP3/BP4 rationale for interpretation.
3 Likely pathogenic · 2 Uncertain significance · 1 Pathogenic.
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. BRCA1, a tumor suppressor involved in the DNA damage response, is mutated in various cancer types.
This variant has not previously been reported in somatic cancers (COSMIC).
This variant does not lie in a statistically significant hotspot.
ACMG/AMP criteria under ClinGen BRCA1 VCEP v1.2.0, with the data and sources behind each one.
28 criteria with recorded statuses: 2 met · 8 not met · 7 not assessed · 11 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
The BRCA1 c.5200T>A (p.Phe1734Ile; p.F1734I) variant has not been observed in COSMIC and has been reported in ClinVar, where the ClinGen ENIGMA BRCA1/2 expert panel classifies it as likely pathogenic.
This variant is absent from gnomAD v2.1 and gnomAD v4.1, supporting rarity, although the ENIGMA PM2_Supporting rule was not formally established from the available depth-specific evidence.
In a calibrated BRCA1 functional study, saturation genome editing showed loss of function similar to pathogenic control variants, and the ENIGMA BRCA1/2 specification assigns PS3 at Strong strength.
This missense change is located in the BRCA1 BRCT repeats; REVEL is 0.871, but under the ENIGMA computational rule the observed BayesDel score of 0.242362 and SpliceAI max delta score of 0.00 do not meet PP3 or BP4 thresholds.
No criteria match.
ENIGMA BRCA1/2 PS3 Strong for calibrated damaging functional evidence.
ENIGMA BRCA1/2 PP3 for domain missense variants requires BayesDel >=0.28, or SpliceAI >=0.2 for splicing predictions.
ENIGMA BRCA1/2 PP4 likelihood-ratio rule.
ENIGMA BRCA1/2 BA1 population frequency rule.
ENIGMA BRCA1/2 BS1 population frequency rule.
ENIGMA BRCA1/2 BS3 requires well-established studies showing no damaging effect.
ENIGMA BRCA1/2 BP1_Strong rule.
ENIGMA BRCA1/2 BP4 for domain missense variants requires BayesDel <=0.15 and SpliceAI <=0.1.
ENIGMA BRCA1/2 BP5 likelihood-ratio rule.
ENIGMA BRCA1/2 PS1/PS1_Moderate/PS1_Supporting comparator-based rule.
ENIGMA BRCA1/2 PS4 requires significant enrichment in affected individuals versus controls.
ENIGMA BRCA1/2 PM2_Supporting rarity rule.
ENIGMA BRCA1/2 PM3 point-based recessive disease rule.
ENIGMA BRCA1/2 PP1 likelihood-ratio segregation rule.
ENIGMA BRCA1/2 BS2 point-based rule.
ENIGMA BRCA1/2 BS4 likelihood-ratio non-segregation rule.
ENIGMA BRCA1/2 PVS1 applies to null variants at appropriate strength; this missense variant does not meet that entry criterion.
Not applicable in ENIGMA BRCA1/2 specification.
Not applicable in ENIGMA BRCA1/2 specification.
Not applicable in ENIGMA BRCA1/2 specification.
ENIGMA BRCA1/2 PM5_PTC rule.
Not applicable in ENIGMA BRCA1/2 specification.
Not applicable in ENIGMA BRCA1/2 specification.
Not applicable in ENIGMA BRCA1/2 specification.
Not applicable in ENIGMA BRCA1/2 specification.
Not applicable in ENIGMA BRCA1/2 specification.
ENIGMA BRCA1/2 BP7 rule.
Every interpreted variant in BRCA1, mapped onto the exon structure of NM_007294.3. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
Absent from gnomAD v4.1.
Absent from gnomAD v2.1.
ENIGMA BRCA1/2 PP3 for domain missense variants requires BayesDel >=0.28, or SpliceAI >=0.2 for splicing predictions.
ENIGMA BRCA1/2 BP4 for domain missense variants requires BayesDel <=0.15 and SpliceAI <=0.1.
ENIGMA BRCA1/2 BP7 rule.
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.871. BayesDel score = 0.242362.
9 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata. None of the listed paper records explicitly indicates that the variant is named.
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
Absent from gnomAD v4.1.
Absent from gnomAD v2.1.
This variant has been reported in ClinVar as Likely pathogenic (3 clinical laboratories) and as Uncertain significance (2 clinical laboratories) and as Pathogenic (1 clinical laboratory) and as Likely Pathogenic by ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen (expert panel). (ClinVarID = 232047)
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.871. BayesDel score = 0.242362.
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. BRCA1, a tumor suppressor involved in the DNA damage response, is mutated in various cancer types.
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
This variant does not lie in a statistically significant hotspot.