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 benign. Select a step to read what it means.
Benign.A benign classification under the recorded framework.
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.
No pathogenic criterion marked as applied in the recorded assessment.
This variant exceeds the ENIGMA BS1 threshold for benign population frequency. The grpmax FAF is 0.00024454 in gnomAD v2.1 and 0.00028752 in gnomAD v4.1, both above the BS1 threshold of 0.0001 in a non-founder population.
A calibrated functional study summarized by ENIGMA showed no damaging effect on protein function for this variant. ENIGMA Table 9 reports BRCA1 c.1233T>G (p.Asp411Glu) as BS3 Strong because one calibrated study found protein function similar to benign control variants.
This missense variant is outside the BRCA1 clinically important domains used by ENIGMA and is not predicted to affect splicing. Asp411 lies outside the RING (aa 2-101), coiled-coil (aa 1391-1424), and BRCT (aa 1650-1857) domains, and SpliceAI shows a maximum delta score of 0.07, which is below the 0.1 threshold. This meets BP1_Strong.
Expert panel ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen classified as Benign.
ENIGMA BRCA1 and BRCA2 Specification v1.2.0 final-classification framework using 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: 41 / 1,614,214 alleles. Recorded AF 2.53994e-05. Recorded homozygote count 0.
This variant is present in gnomAD v2.1 (AF= 4.25197e-05; MAF= 0.00425%, 12/282222 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000441165; MAF= 0.04412%, 11/24934 alleles, homozygotes = 0); grpmax FAF= 0.00024454.
No SpliceAI or REVEL score is recorded in the fields used for this tile.
A ClinVar laboratory submission summary was not recorded.
OncoKB has not reviewed this specific variant; no variant-level oncogenicity or biological effect is available. Gene-level context: BRCA1, a tumor suppressor involved in the DNA damage response, is mutated in various cancer types.
No COSMIC evidence statement is recorded in this case.
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: 4 met · 4 not met · 9 not assessed · 11 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
The BRCA1 c.1233T>G (p.Asp411Glu; p.D411E) variant has not been reported in COSMIC and has been reported in ClinVar, including a Benign expert-panel classification from ClinGen ENIGMA.
This variant is present in population databases, with gnomAD grpmax FAF values of 0.00024454 in v2.1 and 0.00028752 in v4.1, both above the ENIGMA BS1 threshold of 0.0001 and below the BA1 threshold of 0.001.
A calibrated functional study summarized by ENIGMA showed protein function similar to benign control variants for BRCA1 p.Asp411Glu, supporting BS3_Strong.
Asp411Glu lies outside the BRCA1 RING, coiled-coil, and BRCT domains, and SpliceAI predicts no significant splice effect with a maximum delta score of 0.07, which is below the 0.1 threshold used for BP1_Strong.
No criteria match.
ENIGMA BS1 applies at Strong when FAF >0.0001.
ENIGMA BS3 applies when well-established functional studies show no damaging effect on protein function.
ENIGMA BP1_Strong applies to missense variants outside clinically important domains with SpliceAI <=0.1.
ENIGMA PS3 requires well-established functional studies supportive of a damaging effect.
ENIGMA PM2_Supporting requires absence from controls in gnomAD with adequate coverage.
ENIGMA PP3 requires BayesDel >=0.28 for missense variants inside clinically important domains and/or SpliceAI >=0.2 for predicted splice impact.
ENIGMA BA1 requires FAF >0.001 in a non-founder population.
ENIGMA PS1 requires a previously classified pathogenic or likely pathogenic reference variant with the same protein or splicing consequence.
ENIGMA PS4 requires statistically significant enrichment in affected individuals compared with controls.
ENIGMA PM3 is reserved for BRCA1/2-related Fanconi anemia contexts with point-based scoring.
ENIGMA PP1 requires quantitative co-segregation evidence with likelihood-ratio-based strength assignment.
ENIGMA PP4 uses variant-level clinical-history likelihood ratios toward pathogenicity.
ENIGMA BS4 requires quantitative lack-of-segregation evidence with likelihood-ratio-based strength assignment.
ENIGMA BP5 uses variant-level clinical-history likelihood ratios against pathogenicity.
ENIGMA BP7 for missense variants depends on RNA evidence showing no damaging effect on transcript profile.
ENIGMA BRCA1/2 PVS1 applies to qualifying loss-of-function variants, not to this missense substitution.
Criterion not applicable in ENIGMA BRCA1/2 specification.
Criterion not applicable in ENIGMA BRCA1/2 specification.
Criterion not applicable in ENIGMA BRCA1/2 specification.
ENIGMA PM5 for BRCA1/2 is exon-specific PM5_PTC for qualifying truncating variants.
Criterion not applicable in ENIGMA BRCA1/2 specification.
Criterion not applicable in ENIGMA BRCA1/2 specification.
Criterion not applicable in ENIGMA BRCA1/2 specification.
Criterion not applicable in ENIGMA BRCA1/2 specification.
Criterion not applicable in ENIGMA BRCA1/2 specification.
For this missense variant outside a clinically important domain, ENIGMA directs use of BP1 rather than BP4.
Every interpreted variant in BRCA1, mapped onto the exon structure of NM_007294.4. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
| African/African American30 / 75,080 | 0.0004 |
| Remaining individuals6 / 62,506 | 9.6e-05 |
| Admixed American4 / 60,014 | 6.7e-05 |
| European (non-Finnish)1 / 1,180,036 | 8.5e-07 |
| African/African American11 / 24,934 | 0.00044 |
| Admixed American1 / 35,410 | 2.8e-05 |
This variant is present in gnomAD v4.1 (AF= 2.53994e-05; MAF= 0.00254%, 41/1614214 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000399574; MAF= 0.03996%, 30/75080 alleles, homozygotes = 0); grpmax FAF= 0.00028752.
This variant is present in gnomAD v2.1 (AF= 4.25197e-05; MAF= 0.00425%, 12/282222 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000441165; MAF= 0.04412%, 11/24934 alleles, homozygotes = 0); grpmax FAF= 0.00024454.
ENIGMA PP3 requires BayesDel >=0.28 for missense variants inside clinically important domains and/or SpliceAI >=0.2 for predicted splice impact.
ENIGMA BP7 for missense variants depends on RNA evidence showing no damaging effect on transcript profile.
For this missense variant outside a clinically important domain, ENIGMA directs use of BP1 rather than BP4.
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.07).
0 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata.
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.
This variant is present in gnomAD v4.1 (AF= 2.53994e-05; MAF= 0.00254%, 41/1614214 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000399574; MAF= 0.03996%, 30/75080 alleles, homozygotes = 0); grpmax FAF= 0.00028752.
This variant is present in gnomAD v2.1 (AF= 4.25197e-05; MAF= 0.00425%, 12/282222 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000441165; MAF= 0.04412%, 11/24934 alleles, homozygotes = 0); grpmax FAF= 0.00024454.
This variant has been reported in ClinVar as Likely benign (5 clinical laboratories) and as Benign (4 clinical laboratories) and as Uncertain significance (2 clinical laboratories) and as Benign by ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen (expert panel).
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.07).
OncoKB has not reviewed this specific variant; no variant-level oncogenicity or biological effect is available. Gene-level context: 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.