About BRIP1
No gene-level summary was recorded for this case.
Previous versions
Variant interpretation report
BRIP1 c.1794+19T>C, p.?
Classification
Uncertain significance
Variant description:
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.
In plain language
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.
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 Not recorded. 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: 1
Benign evidence criteria: 1
Pathogenic criteria applied · 1
PM2Supporting
PM2 · supporting
NM_032043.3:c.1794+19T>C is present at extremely low frequency in gnomAD (v2.1 AF = 0.00389%, 11/282,822 alleles; v4.1 AF = 0.00285%, 46/1,612,392 alleles), well below the 0.1% PM2 threshold. The variant is absent from most subpopulations, has 0 homozygotes, and has a grpmax FAF of 1.122e-05. Observed primarily in the Ashkenazi Jewish population (ASJ AF = 0.058%) but remains rare even in this subpopulation.
Benign criteria applied · 1
BP4Supporting
BP4 · supporting
Multiple lines of computational evidence support a benign interpretation. SpliceAI predicts no significant splicing impact for NM_032043.3:c.1794+19T>C (max delta score = 0.10). The variant is located at intron position +19, well outside the canonical splice donor/acceptor consensus. No in silico tool predicts a deleterious effect on splicing.
Recorded classification: Uncertain significance
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, which maps to VUS.
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
46 / 1,612,392 alleles
gnomAD v4.1: 46 / 1,612,392 alleles. Recorded AF 2.8529e-05. Recorded homozygote count 0.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 3.88937e-05; MAF= 0.00389%, 11/282822 alleles, homozygotes = 0) and has highest observed frequency in the Ashkenazi Jewish population (AF= 0.000578704; MAF= 0.05787%, 6/10368 alleles, homozygotes = 0); grpmax FAF= 1.122e-05.
gnomAD-Canada
Not available in gnomAD-Canada v1.0.
SpliceAI score
0.100 maximum delta
Recorded SpliceAI maximum delta score: 0.100. Refer to the recorded PP3/BP4 rationale for interpretation.
ClinVar submissions
3 reported laboratory submissions
3 Likely benign. ClinVar API review status: criteria provided, multiple submitters, no conflicts.
Context only
ClinVar ↗
No screenshot for this evidence
Functional evidence
Not recorded
No standalone functional evidence summary is recorded in evidence_summary.functional.
No listed criterion applied
OncoKB ↗
Somatic evidence
No matching record reported
This variant has not previously been reported in somatic cancers (COSMIC).
Context only
COSMIC ↗
For specialists
Technical detail
ACMG/AMP criteria under Not recorded, with the data and sources behind each one.
29 criteria with recorded statuses: 2 met · 13 not met · 4 not assessed · 10 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Met
Not met
Not assessed
Not applicable
NM_032043.3:c.1794+19T>C is a deep intronic substitution in BRIP1 intron 12 with no predicted effect on splicing (SpliceAI max delta = 0.10).
The variant is extremely rare in population databases (gnomAD v2.1 AF = 0.00389%, v4.1 AF = 0.00285%), meeting PM2 at supporting level.
Multiple lines of computational evidence predict no deleterious splicing effect, meeting BP4 at supporting benign level.
ClinVar reports Likely benign classification by 3 clinical laboratories (GeneDx, Color Health, Labcorp/Invitae), though the 1-star review status does not independently meet BP6 at supporting level under current PP5/BP6 guidance.
No functional studies, case-control data, cosegregation data, de novo reports, or variant-specific literature exist for this variant.
With one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP4), the evidence is balanced and insufficient to classify as either Likely Pathogenic or Likely Benign. The variant is classified as a Variant of Uncertain Significance (VUS) under generic ACMG/AMP 2015 combination rules.
No criteria match.
Met · 2
PM2 SupportingNM_032043.3:c.1794+19T>C is present at extremely low frequency in gnomAD (v2.1 AF = 0.00389%, 11/282,822 alleles; v4.1 AF = 0.00285%, 46/1,612,392 alleles), well below the 0.1% PM2 threshold. The variant is absent from most subpopulations, has 0 homozygotes, and has a grpmax FAF of 1.122e-05. Observed primarily in the Ashkenazi Jewish population (ASJ AF = 0.058%) but remains rare even in this subpopulation. Details ▾Hide ▴
Evidence considered
- gnomAD v2.1: AF = 3.89e-05 (0.00389%)
- 11/282
- 822 alleles
- 0 homozygotes
- gnomAD v4.1: AF = 2.85e-05 (0.00285%)
- 46/1
- 612
- 392 alleles
- grpmax FAF = 1.122e-05 (v2.1)
- Highest subpopulation AF: Ashkenazi Jewish 0.058% (6/10
- 368 in v2.1
- 19/29
- 592 in v4.1)
- Absent from African
- Admixed American
- East Asian
- and Finnish populations in v2.1
Still missing
- PM2 strength is attenuated for deep intronic variants with no predicted functional impact
- rarity alone is weak evidence of pathogenicity for this variant class
Sources
BP4 SupportingMultiple lines of computational evidence support a benign interpretation. SpliceAI predicts no significant splicing impact for NM_032043.3:c.1794+19T>C (max delta score = 0.10). The variant is located at intron position +19, well outside the canonical splice donor/acceptor consensus. No in silico tool predicts a deleterious effect on splicing. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta = 0.10 across all categories (acceptor gain
- acceptor loss
- donor gain
- donor loss)
- Variant located at intronic +19 position
- outside the highly conserved splice donor region
- No in silico prediction tool suggests splicing alteration
Sources
Not met · 13 · evaluated, threshold not reached
PS2 No de novo evidence is available for NM_032043.3:c.1794+19T>C. No publications report de novo occurrence of this variant, and no de novo data are present in ClinVar submissions. Details ▾Hide ▴
Evidence considered
- No de novo reports identified in ClinVar submissions
- literature
- or curated databases
Still missing
- De novo status cannot be assessed without parental genotype data
PS3 No functional studies have been performed on NM_032043.3:c.1794+19T>C. No experimental data exist for this specific variant or for a systematically characterized range that includes this intronic position. Domain-level or gene-level functional characterization does not satisfy PS3 requirements. Details ▾Hide ▴
Evidence considered
- No variant-specific functional assays identified in the literature
- ClinVar submissions
- or curated functional databases
- No systematic range characterization (tiling screen
- saturation mutagenesis
- systematic truncation series) spanning intron 12 position +19
Still missing
- Functional characterization of this specific intronic variant has not been performed
PS4 No case-control or case series data are available for NM_032043.3:c.1794+19T>C. The papers flagged for PS4 evaluation (PMID:18163131, PMID:24366376, PMID:24366402, PMID:31429903, PMID:35802134) are general guidelines and review articles that do not report variant-specific case observations. Details ▾Hide ▴
Evidence considered
- No variant-specific case-control or case series identified in literature review
- Papers triaged as PS4 candidates are general breast cancer susceptibility or screening guideline publications
- not variant-specific case reports
Still missing
- Case-control or case series data for this specific variant are not available
PM6 No de novo evidence is available for NM_032043.3:c.1794+19T>C. No publications or database entries report de novo occurrence of this variant with confirmed maternity and paternity. Details ▾Hide ▴
Evidence considered
- No de novo reports identified in ClinVar
- literature
- or curated databases
Still missing
- Parental genotype data unavailable
- de novo status cannot be assessed
PP3 Multiple lines of computational evidence do not support a deleterious effect. SpliceAI max delta score is 0.10, indicating no predicted splicing impact. REVEL and BayesDel scores are not available for this intronic variant (not applicable to non-coding changes). HCI prior probability is not supported for BRIP1. No in silico evidence supports pathogenicity. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta = 0.10 (no significant splice-altering effect predicted)
- REVEL: not applicable (intronic variant
- no missense score)
- BayesDel: not applicable (intronic variant
- no score)
- HCI prior: gene not supported (BRIP1 not in HCI panel)
Sources
PP4 No patient phenotype or clinical data are available to evaluate whether the proband's presentation is specific for BRIP1-related disease. PP4 requires that the patient's phenotype or family history is highly specific for a disease with a single genetic etiology. Details ▾Hide ▴
Evidence considered
- No patient phenotype
- family history
- or clinical data provided in the case materials
Still missing
- Patient phenotype and family history data are not available for evaluation
PP5 ClinVar classification for NM_032043.3:c.1794+19T>C is Likely benign (Variation ID 377594), not pathogenic. Additionally, the review status is 'criteria provided, single submitter' (1-star), which does not meet the 3-star expert panel threshold required for PP5 application. No reputable source has classified this variant as pathogenic. Details ▾Hide ▴
Evidence considered
- ClinVar Variation ID 377594: Likely benign (3 clinical laboratories)
- Review status: criteria provided
- single submitter (1-star)
- No expert panel
- practice guideline
- or database has classified this variant as pathogenic
Sources
BA1 NM_032043.3:c.1794+19T>C has a gnomAD v2.1 total allele frequency of 0.00389% (3.89e-05), which is far below the 1% BA1 threshold for a benign standing variant. The variant is too rare to meet BA1. Details ▾Hide ▴
Evidence considered
- gnomAD v2.1 AF = 0.00389% (< 1% BA1 threshold)
- gnomAD v4.1 AF = 0.00285% (< 1% BA1 threshold)
- Highest subpopulation AF (ASJ) = 0.058% (< 1% BA1 threshold)
Sources
BS1 NM_032043.3:c.1794+19T>C has a gnomAD v2.1 total allele frequency of 0.00389%, which is below the 0.3% BS1 threshold under generic ACMG rules. The variant frequency does not exceed the expected prevalence for BRIP1-associated disorders. Details ▾Hide ▴
Evidence considered
- gnomAD v2.1 AF = 0.00389% (< 0.3% BS1 threshold)
- gnomAD v4.1 AF = 0.00285% (< 0.3% BS1 threshold)
- Highest subpopulation AF (ASJ v4.1) = 0.064% (< 0.3% BS1 threshold)
Sources
BS2 No evidence that NM_032043.3:c.1794+19T>C has been observed in a healthy adult individual as homozygous or in trans with a known pathogenic BRIP1 variant. gnomAD reports 0 homozygotes across both v2.1 and v4.1. BS2 requires specific observation in a healthy control context. Details ▾Hide ▴
Evidence considered
- gnomAD v2.1: 0 homozygotes (11 heterozygous alleles)
- gnomAD v4.1: 0 homozygotes (46 heterozygous alleles)
- No reports of this variant in trans with a pathogenic BRIP1 variant in a healthy individual
Still missing
- Specific observation in healthy adult controls with full phenotype data not available
Sources
BS3 No functional studies demonstrating no deleterious effect have been performed for NM_032043.3:c.1794+19T>C. BS3 requires well-established in vitro or in vivo functional studies showing no damaging effect on protein function or splicing. Details ▾Hide ▴
Evidence considered
- No functional studies identified for this variant or for a characterized range including intron 12 position +19
Still missing
- No functional data available to assess BS3
BP6 Three clinical laboratories (GeneDx, Color Health, Labcorp/Invitae) independently classify NM_032043.3:c.1794+19T>C as Likely benign in ClinVar (Variation ID 377594). However, the aggregate ClinVar review status is 'criteria provided, single submitter' (1-star), which does not meet the 3-star expert panel threshold required for BP6 application at supporting level under current PP5/BP6 guidance. The available submissions are concordant for a benign interpretation but lack expert panel review. Details ▾Hide ▴
Evidence considered
- ClinVar Variation ID 377594: Likely benign by 3 clinical laboratories (GeneDx SCV000512420
- Color Health SCV000684158
- Labcorp/Invitae SCV002408093)
- Review status: criteria provided
- single submitter (1-star)
- All 3 submissions concordant for Likely benign classification
- Does not meet 3-star expert panel threshold for BP6 application
Still missing
- Expert panel review of this variant would strengthen or confirm the benign classification
Sources
PS5 No reputable source has classified NM_032043.3:c.1794+19T>C as pathogenic. The ClinVar classification is Likely benign (ClinVar Variation ID 377594), and no source asserts pathogenicity. Details ▾Hide ▴
Evidence considered
- ClinVar Variation ID 377594: classification is Likely benign
- not pathogenic
- No expert panel
- practice guideline
- or reputable database has classified this variant as pathogenic
Sources
Not assessed · 4 · no assessment recorded
PP1 No cosegregation data are available for NM_032043.3:c.1794+19T>C. No family studies or pedigrees have been reported in the literature or databases. Details ▾Hide ▴
Evidence considered
- No cosegregation or family study data identified
Still missing
- Family segregation data are not available for this variant
BS4 No cosegregation data are available for NM_032043.3:c.1794+19T>C. BS4 requires lack of cosegregation with disease in affected family members, which cannot be evaluated without family studies. Details ▾Hide ▴
Evidence considered
- No family segregation data available
Still missing
- Family segregation data are not available
BP2 No data are available on whether NM_032043.3:c.1794+19T>C has been observed in trans with a known pathogenic BRIP1 variant. BP2 requires specific observation in trans in an individual without disease features. Details ▾Hide ▴
Evidence considered
- No data on trans configuration with pathogenic BRIP1 variants available
Still missing
- Observation in trans with a pathogenic variant not assessed
BP5 No information is available regarding an alternate molecular basis for disease in the proband. BP5 requires a pathogenic variant in an alternative gene that explains the patient's phenotype. Details ▾Hide ▴
Evidence considered
- No data on alternate molecular diagnosis available
Still missing
- Patient genotype data for other disease-associated genes not available
Not applicable · 10· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 N/ANM_032043.3:c.1794+19T>C is a deep intronic substitution (intron 12, +19 position) that does not fall into the ClinGen PVS1 null-variant buckets (nonsense, frameshift, or canonical ±1,2 splice consensus variants). SpliceAI max delta score of 0.10 confirms no predicted splicing impact. PVS1 is not applicable to this variant class. Details ▾Hide ▴
Evidence considered
- Variant is intronic at position +19
- outside the canonical splice donor/acceptor ±1
- 2 positions
- SpliceAI max delta 0.10 — no predicted splice-altering effect
- ClinGen PVS1 decision framework (PMC6185798) does not include deep intronic variants outside the splice consensus
Sources
PS1 N/AThis is an intronic variant with no amino acid change. PS1 requires the same amino acid change as an established pathogenic variant and is not applicable to non-coding variants. Details ▾Hide ▴
Evidence considered
- Intronic variant c.1794+19T>C produces no amino acid change (NP_114432.2:p.?)
PM1 N/AThis is a deep intronic variant (c.1794+19T>C) that does not alter protein sequence. PM1 requires location in a mutational hotspot or critical functional domain at the protein level. An intronic variant outside splice consensus regions does not qualify. Details ▾Hide ▴
Evidence considered
- Intronic variant at position +19 does not map to any protein domain or residue
- Cancerhotspots.org: not a residue-level variant
- no hotspot identified
PM3 N/ASkipped per instructions: no data on phase-confirmed trans configuration with a pathogenic variant; PM3 is only applicable when both alleles carry pathogenic variants. Details ▾Hide ▴
No further detail was recorded.
PM4 N/ASkipped per instructions: this variant is a substitution, not a non-frameshift indel or stop-loss variant causing protein length change. Details ▾Hide ▴
No further detail was recorded.
PM5 N/ANM_032043.3:c.1794+19T>C is an intronic variant with no amino acid change (NP_114432.2:p.?). PM5 requires a different missense change at the same codon as an established pathogenic variant, which cannot be assessed for a non-coding intronic variant. Details ▾Hide ▴
Evidence considered
- Intronic variant
- no protein residue position determinable
- pm5_candidates.json: eligible_for_classic_pm5_search = false
- protein consequence = p.?
Sources
pm5_candidates
PP2 N/APP2 applies to missense variants in genes where missense variants are a common disease mechanism and benign missense variation is rare. NM_032043.3:c.1794+19T>C is an intronic variant, not a missense change, and therefore PP2 does not apply. Details ▾Hide ▴
Evidence considered
- Intronic variant
- not a missense change
BP1 N/ABP1 applies specifically to missense variants in genes where truncating variants are a predominant disease mechanism. NM_032043.3:c.1794+19T>C is an intronic variant, not a missense change, and BP1 does not apply. Details ▾Hide ▴
Evidence considered
- Intronic variant
- not a missense change
BP3 N/ASkipped per instructions: this variant is a substitution, not an in-frame indel in a repetitive region. Details ▾Hide ▴
No further detail was recorded.
BP7 N/ABP7 applies to synonymous (silent) variants for which splicing prediction algorithms predict no impact. NM_032043.3:c.1794+19T>C is an intronic variant, not a synonymous coding change. BP7 does not apply to intronic substitutions. Details ▾Hide ▴
Evidence considered
- Intronic variant (c.1794+19T>C)
- not a synonymous coding change
- SpliceAI predicts no splice impact
- but BP7 is restricted to synonymous variants per ACMG 2015
Identifiers
- Gene
- BRIP1
- Transcript
- NM_032043.3
- Coding (HGVS c.)
- NM_032043.3:c.1794+19T>C
- Protein (HGVS p.)
- NP_114432.2:p.?
- GRCh38
- chr17:61780821 A>G
- GRCh37
- chr17:59858182 A>G
- ClinVar
- 377594
Gene diagram
Every interpreted variant in BRIP1, mapped onto the exon structure of NM_032043.3. Select a row to find it on the plot.
BRIP1NM_032043.3
Fetching transcript structure from UCSC…
Exons
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Transcript span
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Strand
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Variants mapped
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Source
UCSC ncbiRefSeqCurated
All variants in BRIP1
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Select a row to find it on the plot; use the link to open its page.
| Protein | Location | Classification | Link |
|---|
gnomAD v4.1
46 / 1,612,392 alleles
AF 2.85e-05 · 0 homozygotes · FAF 9.55e-06
gnomAD v2.1
11 / 282,822 alleles
AF 3.89e-05 · 0 homozygotes · FAF 1.12e-05
gnomAD-Canada v1.0
Allele count data not recorded
By genetic ancestry
gnomAD v4.1
AF 2.9e-05 · 46 / 1,612,392 alleles · 0 hom · FAF 9.6e-06
| Ashkenazi Jewish19 / 29,592 | 0.00064 |
| Middle Eastern1 / 6,080 | 0.00016 |
| Remaining individuals8 / 62,452 | 0.00013 |
| European (non-Finnish)18 / 1,178,520 | 1.5e-05 |
0 alternate alleles recorded in 6 other groups: Admixed American, European (Finnish), Amish, East Asian, South Asian, African/African American.
gnomAD v2.1
AF 3.9e-05 · 11 / 282,822 alleles · 0 hom · FAF 1.1e-05
| Ashkenazi Jewish6 / 10,368 | 0.00058 |
| European (non-Finnish)5 / 129,140 | 3.9e-05 |
0 alternate alleles recorded in 6 other groups: African/African American, Admixed American, East Asian, European (Finnish), Remaining individuals, South Asian.
Statements
gnomAD v4.1
This variant is present in gnomAD v4.1 (AF= 2.8529e-05; MAF= 0.00285%, 46/1612392 alleles, homozygotes = 0) and has highest observed frequency in the Ashkenazi Jewish population (AF= 0.000642065; MAF= 0.06421%, 19/29592 alleles, homozygotes = 0); grpmax FAF= 9.55e-06.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 3.88937e-05; MAF= 0.00389%, 11/282822 alleles, homozygotes = 0) and has highest observed frequency in the Ashkenazi Jewish population (AF= 0.000578704; MAF= 0.05787%, 6/10368 alleles, homozygotes = 0); grpmax FAF= 1.122e-05.
gnomAD-Canada
Not available in gnomAD-Canada v1.0.
SpliceAI and Pangolin
Other predictors
- REVEL
- Not available
- BayesDel
- Not available
How the predictions were used
BP4 SupportingMultiple lines of computational evidence support a benign interpretation. SpliceAI predicts no significant splicing impact for NM_032043.3:c.1794+19T>C (max delta score = 0.10). The variant is located at intron position +19, well outside the canonical splice donor/acceptor consensus. No in silico tool predicts a deleterious effect on splicing. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta = 0.10 across all categories (acceptor gain
- acceptor loss
- donor gain
- donor loss)
- Variant located at intronic +19 position
- outside the highly conserved splice donor region
- No in silico prediction tool suggests splicing alteration
Sources
PP3 Multiple lines of computational evidence do not support a deleterious effect. SpliceAI max delta score is 0.10, indicating no predicted splicing impact. REVEL and BayesDel scores are not available for this intronic variant (not applicable to non-coding changes). HCI prior probability is not supported for BRIP1. No in silico evidence supports pathogenicity. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta = 0.10 (no significant splice-altering effect predicted)
- REVEL: not applicable (intronic variant
- no missense score)
- BayesDel: not applicable (intronic variant
- no score)
- HCI prior: gene not supported (BRIP1 not in HCI panel)
Sources
BP7 N/ABP7 applies to synonymous (silent) variants for which splicing prediction algorithms predict no impact. NM_032043.3:c.1794+19T>C is an intronic variant, not a synonymous coding change. BP7 does not apply to intronic substitutions. Details ▾Hide ▴
Evidence considered
- Intronic variant (c.1794+19T>C)
- not a synonymous coding change
- SpliceAI predicts no splice impact
- but BP7 is restricted to synonymous variants per ACMG 2015
Statement
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.10).
7 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.
Recorded publications
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PMID 25741868 ↗Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.This is the canonical ACMG/AMP 2015 standards and guidelines for sequence variant interpretation. Describes the classification framework used for this assessment. NM_032043.3:c.1794+19T>C is not mentioned.Does not name this variant
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PMID 18163131 ↗The emerging landscape of breast cancer susceptibility.Stratton MR et al. · 2008Review article describing the landscape of breast cancer susceptibility genes, including BRIP1 as a moderate-penetrance gene. Discusses BRIP1 truncating mutations as low-penetrance breast cancer alleles. NM_032043.3:c.1794+19T>C is not mentioned in this publication.Does not name this variant
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PMID 24366376 ↗Risk assessment, genetic counseling, and genetic testing for BRCA-related cancer in women: U.S. Preventive Services Task Force recommendation statement.Moyer VA et al. · 2014USPSTF recommendation statement on BRCA-related cancer risk assessment, genetic counseling, and genetic testing. Focuses on BRCA1/BRCA2 screening; does not discuss BRIP1 or the variant NM_032043.3:c.1794+19T>C.Does not name this variant
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PMID 24366402 ↗Summaries for patients. Assessing the genetic risk for BRCA-related breast or ovarian cancer in women: recommendations from the U.S. Preventive Services Task Force.2014Patient summary of the USPSTF recommendation on BRCA-related cancer genetic risk assessment. NM_032043.3:c.1794+19T>C is not mentioned in this publication.Does not name this variant
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PMID 31429903 ↗Risk Assessment, Genetic Counseling, and Genetic Testing for BRCA-Related Cancer: US Preventive Services Task Force Recommendation Statement.Updated USPSTF recommendation statement on BRCA-related cancer risk assessment, genetic counseling, and genetic testing. Focuses on BRCA1/BRCA2 population screening recommendations. NM_032043.3:c.1794+19T>C is not mentioned.Does not name this variant
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PMID 35802134 ↗ACMG SF v3.1 list for reporting of secondary findings in clinical exome and genome sequencing: A policy statement of the American College of Medical Genetics and Genomics (ACMG).ACMG SF v3.1 policy statement on secondary findings reporting in clinical exome and genome sequencing. Lists genes recommended for secondary findings reporting; BRIP1 is not included on the secondary findings gene list. NM_032043.3:c.1794+19T>C is not mentioned.Does not name this variant
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PMID 28492532 ↗Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.Sherloc classification framework paper, a refinement of ACMG-AMP variant classification criteria. Provides background on variant classification methodology but does not discuss NM_032043.3:c.1794+19T>C.Does not name this variant
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
gnomAD v4.1
46 / 1,612,392 recorded alleles
Open source ↗
gnomAD v2.1
Captured gnomAD v2.1 source record
Open source ↗
SpliceAI Lookup
Recorded maximum delta 0.100
Open source ↗
ClinVar
3 Likely benign
Open source ↗
COSMIC
Captured COSMIC source record
Open source ↗
All source links
- ClinVar ↗www.ncbi.nlm.nih.gov/clinvar/variation/377594/
- gnomAD v2.1 ↗gnomad.broadinstitute.org/variant/17-59858182-A-G?dataset=gnomad_r2_1
- gnomAD v4.1 ↗gnomad.broadinstitute.org/variant/chr17-61780821-A-G?dataset=gn…
- gnomAD-Canada ↗http://192.168.4.76:8001/variant/17-61780821-A-G
- SpliceAI Lookup ↗spliceailookup.broadinstitute.org/#variant=NM_032043.3%3Ac.1794…
- OncoKB ↗www.oncokb.org/gene/BRIP1/?
- COSMIC ↗cancer.sanger.ac.uk/cosmic/search?q=BRIP1+c.1794+19T%3EC
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= 2.8529e-05; MAF= 0.00285%, 46/1612392 alleles, homozygotes = 0) and has highest observed frequency in the Ashkenazi Jewish population (AF= 0.000642065; MAF= 0.06421%, 19/29592 alleles, homozygotes = 0); grpmax FAF= 9.55e-06.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 3.88937e-05; MAF= 0.00389%, 11/282822 alleles, homozygotes = 0) and has highest observed frequency in the Ashkenazi Jewish population (AF= 0.000578704; MAF= 0.05787%, 6/10368 alleles, homozygotes = 0); grpmax FAF= 1.122e-05.
gnomAD-Canada
Not available in gnomAD-Canada v1.0.
ClinVar
This variant has been reported in ClinVar as Likely benign (3 clinical laboratories). (ClinVarID = 377594)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.10).
Somatic
This variant has not previously been reported in somatic cancers (COSMIC).