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Variant interpretation report

BRCA1 c.1233T>G, p.(Asp411Glu)

NM_007294.4:c.1233T>G NP_009225.1:p.(Asp411Glu) View identifiers
Classification
Benign

Variant description:

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.

In plain language

Gene-level background from the recorded interpretation.

About BRCA1

No gene-level summary was recorded for this case.

LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
01The reasoning

How it was classified

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.

Recorded applied criteria

The applied criteria and their strengths are shown as assessed under the stated framework.

Pathogenic evidence criteria: 0 Benign evidence criteria: 4
Pathogenic criteria applied · 0

No pathogenic criterion marked as applied in the recorded assessment.

Benign criteria applied · 4
BS1Strong
BS1 · strong

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.

BS3Strong
BS3 · strong

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.

BP1Strong
BP1 · strong

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.

BP6Supporting
BP6 · supporting

Expert panel ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen classified as Benign.

Recorded classification: Benign

ENIGMA BRCA1 and BRCA2 Specification v1.2.0 final-classification framework using Table 3 criteria-combination rules

02The sources

Evidence at a glance

Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.

gnomAD v4.1
gnomAD v2.1
Population frequency
41 / 1,614,214 alleles

gnomAD v4.1: 41 / 1,614,214 alleles. Recorded AF 2.53994e-05. Recorded homozygote count 0.

gnomAD v2.1

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 screenshot for this evidence
Computational predictions
Not recorded

No SpliceAI or REVEL score is recorded in the fields used for this tile.

No listed criterion applied
Functional evidence
Statement 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.

COSMIC
Cancer Hotspots
Somatic evidence
Not assessed

No COSMIC evidence statement is recorded in this case.

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.

For specialists

Technical detail

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.

Met Not met Not assessed Not applicable

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.

Met · 4

BS1 StrongThis 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. Details ▾Hide ▴
Rule
ENIGMA BS1 applies at Strong when FAF >0.0001.
Evidence considered
  • gnomAD v2.1: African/African American AF 0.000441165
  • grpmax FAF 0.00024454.
  • gnomAD v4.1: African/African American AF 0.000399574
  • grpmax FAF 0.00028752.
Sources
BS3 StrongA 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. Details ▾Hide ▴
Rule
ENIGMA BS3 applies when well-established functional studies show no damaging effect on protein function.
Evidence considered
  • ENIGMA Table 9 entry: BRCA1 c.1233T>G p.(Asp411Glu)
  • BS3 Strong
  • one calibrated study
  • protein function similar to benign controls.
Sources
cspec ↗vcep_specifications_table9_v1_2_2024_11_18
BP1 StrongThis 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. Details ▾Hide ▴
Rule
ENIGMA BP1_Strong applies to missense variants outside clinically important domains with SpliceAI <=0.1.
Evidence considered
  • Protein position 411 is outside ENIGMA-defined clinically important domains.
  • SpliceAI max delta score 0.07 <= 0.1.
Sources
cspec ↗spliceai ↗vcep_appendices_v1_2_2024_11_18
BP6 SupportingExpert panel ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen classified as Benign. Details ▾Hide ▴
Rule
Criterion not applicable in ENIGMA BRCA1/2 specification.
Evidence considered
  • CSPEC marks BP6 as not applicable.
  • ClinVar expert panel classification
Sources

Not met · 4 · evaluated, threshold not reached

PS3 Available functional evidence does not support a damaging effect. ENIGMA Table 9 summarizes this variant as showing protein function similar to benign control variants in a calibrated study, so PS3 is not met. Details ▾Hide ▴
Rule
ENIGMA PS3 requires well-established functional studies supportive of a damaging effect.
Evidence considered
  • Table 9 entry for BRCA1 c.1233T>G p.(Asp411Glu): BS3 Strong
  • reported by one calibrated study to exhibit protein function similar to benign control variants.
Sources
cspec ↗vcep_specifications_table9_v1_2_2024_11_18
PM2 This variant is not absent from population databases. It is present in gnomAD v2.1 at AF 0.0000425 with grpmax FAF 0.00024454 and in gnomAD v4.1 at AF 0.0000254 with grpmax FAF 0.00028752, so the ENIGMA requirement for absence from controls is not met. Details ▾Hide ▴
Rule
ENIGMA PM2_Supporting requires absence from controls in gnomAD with adequate coverage.
Evidence considered
  • gnomAD v2.1: 12/282222 alleles
  • grpmax FAF 0.00024454.
  • gnomAD v4.1: 41/1614214 alleles
  • grpmax FAF 0.00028752.
Sources
PP3 Available predictive evidence does not support a pathogenic computational call under the ENIGMA BRCA1 rules. SpliceAI predicts no significant splice impact with a maximum delta score of 0.07, which is below the 0.2 PP3 threshold, and this variant is outside the BRCA1 clinically important domains used for missense PP3 application. Details ▾Hide ▴
Rule
ENIGMA PP3 requires BayesDel >=0.28 for missense variants inside clinically important domains and/or SpliceAI >=0.2 for predicted splice impact.
Evidence considered
  • SpliceAI max delta score 0.07.
  • Protein position 411 is outside the BRCA1 RING (aa 2-101)
  • coiled-coil (aa 1391-1424)
  • and BRCT (aa 1650-1857) domains.
Still missing
  • No qualifying BayesDel-based pathogenic call was identified from the available materials.
Sources
cspec ↗spliceai ↗vcep_appendices_v1_2_2024_11_18
BA1 The population frequency does not reach the ENIGMA BA1 threshold. The highest observed grpmax FAF is 0.00028752 in gnomAD v4.1, which is below the BA1 cutoff of 0.001. Details ▾Hide ▴
Rule
ENIGMA BA1 requires FAF >0.001 in a non-founder population.
Evidence considered
  • gnomAD v2.1 grpmax FAF 0.00024454.
  • gnomAD v4.1 grpmax FAF 0.00028752.
Sources

Not assessed · 9 · no assessment recorded

PS1 No evidence was identified that this variant produces the same protein change or the same predicted splicing effect as a previously classified pathogenic or likely pathogenic BRCA1 variant, so PS1 was not applied. Details ▾Hide ▴
Rule
ENIGMA PS1 requires a previously classified pathogenic or likely pathogenic reference variant with the same protein or splicing consequence.
Evidence considered
  • ClinVar reports this variant itself
  • but no qualifying pathogenic reference variant with the same amino acid change or same splicing outcome was identified from the available evidence.
Still missing
  • A dedicated same-amino-acid or same-splicing reference variant lookup was not identified in the available materials.
Sources
PS4 No case-control study or other prevalence analysis was identified showing this variant is significantly enriched in affected individuals compared with controls, so PS4 was not applied. Details ▾Hide ▴
Rule
ENIGMA PS4 requires statistically significant enrichment in affected individuals compared with controls.
Evidence considered
  • ClinVar contains submissions for this variant
  • including an expert panel benign classification
  • but this is not a PS4 case-control dataset.
  • COSMIC did not report this variant in somatic cancers.
Still missing
  • No qualifying odds ratio and confidence interval were identified.
Sources
PM3 No evidence was identified that this variant has been observed with a second BRCA1 variant in a proband with a phenotype consistent with BRCA1-related Fanconi anemia, so PM3 was not applied. Details ▾Hide ▴
Rule
ENIGMA PM3 is reserved for BRCA1/2-related Fanconi anemia contexts with point-based scoring.
Evidence considered
  • Available records did not provide Fanconi anemia-based phase and phenotype data required for ENIGMA PM3 scoring.
Still missing
  • No qualifying recessive-disease proband data were identified.
Sources
PP1 No quantitative co-segregation data were identified for this variant, so PP1 was not applied. Details ▾Hide ▴
Rule
ENIGMA PP1 requires quantitative co-segregation evidence with likelihood-ratio-based strength assignment.
Evidence considered
  • Available evidence did not include segregation analysis data.
Still missing
  • No pedigree-based likelihood ratio for segregation was identified.
Sources
PP4 No qualifying multifactorial clinical-history likelihood ratio toward pathogenicity was identified for this variant. The available BRCA1 clinical-history LR table did not provide a matching variant-level result, so PP4 was not applied. Details ▾Hide ▴
Rule
ENIGMA PP4 uses variant-level clinical-history likelihood ratios toward pathogenicity.
Evidence considered
  • The available BRCA1 clinical-history LR resource was reviewed
  • but no matching row for this variant was identified.
Still missing
  • No variant-level clinical-history LR >=2.08 was identified.
Sources
cspec ↗vcep_pmid_31853058_brca1_clinical_history_lrPMID:31853058 ↗
BS2 No qualifying evidence was identified showing this variant in enough individuals without features of BRCA1-related Fanconi anemia to reach the ENIGMA BS2 point thresholds, so BS2 was not applied. Details ▾Hide ▴
Rule
ENIGMA BS2 uses a point-based framework tied to absence of recessive-disease features.
Evidence considered
  • Available evidence did not provide the structured proband data required for ENIGMA BS2 scoring.
Still missing
  • No point-based BS2 proband data were identified.
Sources
BS4 No quantitative lack-of-segregation data were identified for this variant, so BS4 was not applied. Details ▾Hide ▴
Rule
ENIGMA BS4 requires quantitative lack-of-segregation evidence with likelihood-ratio-based strength assignment.
Evidence considered
  • Available evidence did not include lack-of-segregation analysis.
Still missing
  • No pedigree-based likelihood ratio against pathogenicity was identified.
Sources
BP5 No qualifying multifactorial clinical-history likelihood ratio against pathogenicity was identified for this variant. The available BRCA1 clinical-history LR table did not provide a matching variant-level result, so BP5 was not applied. Details ▾Hide ▴
Rule
ENIGMA BP5 uses variant-level clinical-history likelihood ratios against pathogenicity.
Evidence considered
  • The available BRCA1 clinical-history LR resource was reviewed
  • but no matching row for this variant was identified.
Still missing
  • No variant-level clinical-history LR <=0.48 was identified.
Sources
cspec ↗vcep_pmid_31853058_brca1_clinical_history_lrPMID:31853058 ↗
BP7 No RNA assay evidence was identified showing that this variant has no effect on mRNA splicing, so BP7 was not applied. Details ▾Hide ▴
Rule
ENIGMA BP7 for missense variants depends on RNA evidence showing no damaging effect on transcript profile.
Evidence considered
  • SpliceAI predicts low splice impact with max delta score 0.07
  • but ENIGMA BP7 requires qualifying RNA evidence for use in missense variants.
Still missing
  • No qualifying variant-specific mRNA study result was identified.
Sources
Not applicable · 11· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 N/AThis is a missense variant, p.(Asp411Glu), and does not fall into the BRCA1 loss-of-function categories used for PVS1 such as nonsense, frameshift, canonical +/-1,2 splice, initiation codon, or exon-level deletion variants. Details ▾Hide ▴
Rule
ENIGMA BRCA1/2 PVS1 applies to qualifying loss-of-function variants, not to this missense substitution.
Evidence considered
  • BRCA1 is eligible for PVS1 in general because loss of function is an established disease mechanism.
  • Variant-level PVS1 assessment indicates this variant is not in a default null-variant bucket.
Sources
cspec ↗pvs1_gene_contextpvs1_variant_assessment
PS2 N/APS2 is not used in this BRCA1 ENIGMA framework. Details ▾Hide ▴
Rule
Criterion not applicable in ENIGMA BRCA1/2 specification.
Evidence considered
  • CSPEC marks PS2 as not applicable.
Sources
PM1 N/APM1 is not used in this BRCA1 ENIGMA framework. Details ▾Hide ▴
Rule
Criterion not applicable in ENIGMA BRCA1/2 specification.
Evidence considered
  • CSPEC marks PM1 as not applicable.
Sources
PM4 N/APM4 is not used in this BRCA1 ENIGMA framework. Details ▾Hide ▴
Rule
Criterion not applicable in ENIGMA BRCA1/2 specification.
Evidence considered
  • CSPEC marks PM4 as not applicable.
Sources
PM5 N/AIn the BRCA1 ENIGMA specification, PM5 is used for protein-terminating variants in eligible exons. This variant is a missense substitution and does not qualify for PM5 under this framework. Details ▾Hide ▴
Rule
ENIGMA PM5 for BRCA1/2 is exon-specific PM5_PTC for qualifying truncating variants.
Evidence considered
  • ENIGMA Table 4 describes PM5_PTC use for protein termination codon variants
  • not for this missense change.
Sources
cspec ↗vcep_specifications_table4_v1_2_2024_11_18
PM6 N/APM6 is not used in this BRCA1 ENIGMA framework. Details ▾Hide ▴
Rule
Criterion not applicable in ENIGMA BRCA1/2 specification.
Evidence considered
  • CSPEC marks PM6 as not applicable.
Sources
PP2 N/APP2 is not used in this BRCA1 ENIGMA framework. Details ▾Hide ▴
Rule
Criterion not applicable in ENIGMA BRCA1/2 specification.
Evidence considered
  • CSPEC marks PP2 as not applicable.
Sources
PP5 N/APP5 is not used in this BRCA1 ENIGMA framework. Details ▾Hide ▴
Rule
Criterion not applicable in ENIGMA BRCA1/2 specification.
Evidence considered
  • CSPEC marks PP5 as not applicable.
Sources
BP2 N/ABP2 is not used in this BRCA1 ENIGMA framework. Details ▾Hide ▴
Rule
Criterion not applicable in ENIGMA BRCA1/2 specification.
Evidence considered
  • CSPEC marks BP2 as not applicable.
Sources
BP3 N/ABP3 is not used in this BRCA1 ENIGMA framework. Details ▾Hide ▴
Rule
Criterion not applicable in ENIGMA BRCA1/2 specification.
Evidence considered
  • CSPEC marks BP3 as not applicable.
Sources
BP4 N/AUnder the ENIGMA BRCA1 rules, BP4 for missense variants is used for variants inside clinically important domains with BayesDel <=0.15 and SpliceAI <=0.1. This variant is outside those domains, so BP4 is not the applicable benign computational code here. Details ▾Hide ▴
Rule
For this missense variant outside a clinically important domain, ENIGMA directs use of BP1 rather than BP4.
Evidence considered
  • Protein position 411 is outside the ENIGMA-defined clinically important domains.
  • SpliceAI max delta score 0.07.
Sources
cspec ↗spliceai ↗vcep_appendices_v1_2_2024_11_18

Identifiers

Gene
BRCA1
Transcript
NM_007294.4
Coding (HGVS c.)
NM_007294.4:c.1233T>G
Protein (HGVS p.)
NP_009225.1:p.(Asp411Glu)
GRCh38
chr17:43094298 A>C
GRCh37
chr17:41246315 A>C

Gene diagram

Every interpreted variant in BRCA1, mapped onto the exon structure of NM_007294.4. Select a row to find it on the plot.

BRCA1NM_007294.4
Fetching transcript structure from UCSC…
gnomAD v4.1 41 / 1,614,214 alleles AF 2.54e-05 · 0 homozygotes · FAF 0.000288
gnomAD v2.1 12 / 282,222 alleles AF 4.25e-05 · 0 homozygotes · FAF 0.000245

By genetic ancestry

gnomAD v4.1

AF 2.5e-05 · 41 / 1,614,214 alleles · 0 hom · FAF 0.00029
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
0 alternate alleles recorded in 6 other groups: European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish.

gnomAD v2.1

AF 4.3e-05 · 12 / 282,222 alleles · 0 hom · FAF 0.00024
African/African American11 / 24,934 0.00044
Admixed American1 / 35,410 2.8e-05
0 alternate alleles recorded in 6 other groups: Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals, South Asian.

Statements

gnomAD v4.1

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.

gnomAD v2.1

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.

Other predictors

REVEL
Not available
BayesDel
Not available

How the predictions were used

PP3 Available predictive evidence does not support a pathogenic computational call under the ENIGMA BRCA1 rules. SpliceAI predicts no significant splice impact with a maximum delta score of 0.07, which is below the 0.2 PP3 threshold, and this variant is outside the BRCA1 clinically important domains used for missense PP3 application. Details ▾Hide ▴
Rule
ENIGMA PP3 requires BayesDel >=0.28 for missense variants inside clinically important domains and/or SpliceAI >=0.2 for predicted splice impact.
Evidence considered
  • SpliceAI max delta score 0.07.
  • Protein position 411 is outside the BRCA1 RING (aa 2-101)
  • coiled-coil (aa 1391-1424)
  • and BRCT (aa 1650-1857) domains.
Still missing
  • No qualifying BayesDel-based pathogenic call was identified from the available materials.
Sources
cspec ↗spliceai ↗vcep_appendices_v1_2_2024_11_18
BP7 No RNA assay evidence was identified showing that this variant has no effect on mRNA splicing, so BP7 was not applied. Details ▾Hide ▴
Rule
ENIGMA BP7 for missense variants depends on RNA evidence showing no damaging effect on transcript profile.
Evidence considered
  • SpliceAI predicts low splice impact with max delta score 0.07
  • but ENIGMA BP7 requires qualifying RNA evidence for use in missense variants.
Still missing
  • No qualifying variant-specific mRNA study result was identified.
Sources
BP4 N/AUnder the ENIGMA BRCA1 rules, BP4 for missense variants is used for variants inside clinically important domains with BayesDel <=0.15 and SpliceAI <=0.1. This variant is outside those domains, so BP4 is not the applicable benign computational code here. Details ▾Hide ▴
Rule
For this missense variant outside a clinically important domain, ENIGMA directs use of BP1 rather than BP4.
Evidence considered
  • Protein position 411 is outside the ENIGMA-defined clinically important domains.
  • SpliceAI max delta score 0.07.
Sources
cspec ↗spliceai ↗vcep_appendices_v1_2_2024_11_18

Statement

In silico

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.

All source links

Statements for reports

The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.

gnomAD v4.1

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.

gnomAD v2.1

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.

ClinVar

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).

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.07).

Functional

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.

Somatic

This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.