About BRAF
No gene-level summary was recorded for this case.
Previous versions
Variant interpretation report
BRAF c.1741A>T, p.(Asn581Tyr)
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 ClinGen BRAF VCEP v2.3.0. 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: 3
Benign evidence criteria: 0
Pathogenic criteria applied · 3
PM2Supporting
PM2 · supporting
The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada v1.0. Per the RASopathy VCEP, absence from gnomAD meets PM2 at Supporting strength (PM2_Supporting).
PP2Supporting
PP2 · supporting
BRAF has a low rate of benign missense variation in gnomAD (missense Z-score well above 3.09) and missense variants are a common mechanism of disease in RASopathies (gain-of-function). PP2 at Supporting strength is appropriate per VCEP specifications.
PP3Supporting
PP3 · supporting
REVEL score is 0.978, which meets the VCEP threshold of ≥0.7 for PP3 at Supporting strength. SpliceAI max delta score is 0.07, indicating no splicing impact that would contradict the disease mechanism.
Benign criteria applied · 0
No benign criterion marked as applied in the recorded assessment.
Recorded classification: Uncertain significance
ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for BRAF Version 2.3.0 v2.3.0 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting, PP2 supporting, PP3 supporting; no rule matched the adjudicated criteria.
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
Not recorded
gnomAD v4.1 allele counts were not recorded for this variant.
gnomAD v2.1
Absent from gnomAD v2.1.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
SpliceAI score
0.070 maximum delta
Recorded SpliceAI maximum delta score: 0.070. Refer to the recorded PP3/BP4 rationale for interpretation.
ClinVar submissions
Not recorded
A ClinVar laboratory submission summary was not recorded.
Context only
ClinVar ↗
Functional evidence
Statement recorded
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Gain-of-function; curated oncogenicity label: Likely Oncogenic.
No listed criterion applied
OncoKB ↗
COSMIC
Cancer Hotspots
Somatic evidence
7 recorded samples
This variant has previously been reported in somatic cancers (COSMIC; COSV56062673, n = 7 times).
Cancer Hotspots
This variant lies in a statistically significant hotspot.
Context only
For specialists
Technical detail
ACMG/AMP criteria under ClinGen BRAF VCEP v2.3.0, with the data and sources behind each one.
26 criteria with recorded statuses: 3 met · 15 not met · 0 not assessed · 8 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Met
Not met
Not assessed
Not applicable
NM_004333.6:c.1741A>T (p.Asn581Tyr) is a missense variant in exon 14 of BRAF, encoding a substitution at a highly conserved residue within the kinase domain.
This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting PM2 at Supporting strength per the ClinGen RASopathy VCEP v2.3.0 (PM2_Supporting).
BRAF exhibits strong constraint against missense variation in gnomAD (missense Z-score >3.09), and missense variants are a common mechanism of RASopathy, meeting PP2 at Supporting strength.
The REVEL in silico prediction score is 0.978, exceeding the VCEP threshold of ≥0.7 for PP3 at Supporting strength. SpliceAI predicts no significant splicing impact (max delta = 0.07).
N581Y has been observed as a somatic variant in multiple cancer types: colorectal cancer cell line HT55 (Seth 2009, PMID:19474002), melanoma cell line WM3912 (Hutchinson 2015, PMID:26084293), and in a cfDNA NSCLC cohort where it was identified as a novel activating mutation by Ba/F3 assay (Negrao 2020, PMID:32540409). N581Y is catalogued in COSMIC (COSV56062673, n=7). OncoKB classifies it as Likely Oncogenic with Likely Gain-of-function effect.
No germline RASopathy probands, de novo occurrences, or family segregation data are available for this variant. VCEP-approved functional assays (BRAF Kinase Activity, MEK/ERK Activation Assays) have no data for N581Y.
The N581 residue lies in a statistically significant hotspot, but is outside the VCEP-specified PM1 domains (P-loop AA 459-474 and CR3 activation segment AA 594-627); PM1 is not met.
No criteria match.
Met · 3
PM2 SupportingThe variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada v1.0. Per the RASopathy VCEP, absence from gnomAD meets PM2 at Supporting strength (PM2_Supporting). Details ▾Hide ▴
Evidence considered
- Absent from gnomAD v2.1 (exomes)
- Absent from gnomAD v4.1 (exomes)
- Absent from gnomAD-Canada v1.0 (genomes)
Sources
PP2 SupportingBRAF has a low rate of benign missense variation in gnomAD (missense Z-score well above 3.09) and missense variants are a common mechanism of disease in RASopathies (gain-of-function). PP2 at Supporting strength is appropriate per VCEP specifications. Details ▾Hide ▴
Evidence considered
- BRAF missense Z-score exceeds 3.09 in gnomAD
- indicating strong constraint against missense variation
- RASopathy disease mechanism is gain-of-function via missense variants
Sources
PP3 SupportingREVEL score is 0.978, which meets the VCEP threshold of ≥0.7 for PP3 at Supporting strength. SpliceAI max delta score is 0.07, indicating no splicing impact that would contradict the disease mechanism. Details ▾Hide ▴
Evidence considered
- REVEL score = 0.978 (≥0.7 threshold)
- SpliceAI max delta = 0.07 (no predicted splicing impact)
Sources
revelspliceai ↗
Not met · 15 · evaluated, threshold not reached
PS1 PS1 requires the same amino acid change as a previously established pathogenic variant. N581Y (p.Asn581Tyr) has been reported in somatic cancer literature (colorectal cancer, melanoma, NSCLC) but has not been established as a germline pathogenic variant in RASopathy. No ClinVar entry classifies N581Y as pathogenic in a germline context. Details ▾Hide ▴
Evidence considered
- N581Y observed in somatic cancer cell lines HT55 (CRC)
- WM3912 (melanoma)
- and cfDNA NSCLC cohort (Negrao 2020)
- but no germline pathogenic classification exists
Still missing
- No germline pathogenic classification for N581Y in ClinVar or RASopathy literature
Sources
PS2 No de novo occurrence of NM_004333.6:c.1741A>T has been reported in a patient with a RASopathy phenotype and confirmed parentage. No proband case data available. Details ▾Hide ▴
Still missing
- No de novo case reports for this variant in RASopathy
PS3 The ClinGen RASopathy VCEP-approved functional assays (BRAF Kinase Activity, MEK Activation Assay, ERK Activation Assay) have no data for N581Y in the approved functional studies spreadsheet. The Ba/F3 cell viability assay identifying N581Y as activating (Negrao 2020, PMID:32540409) is not among the VCEP-approved PS3 assays. IMPACT detection of N581Y with predicted modest kinase activity (Hutchinson 2015, PMID:26084293) does not constitute a validated functional assay. Details ▾Hide ▴
Evidence considered
- N581Y shown as activating in Ba/F3 IL-3 independence assay (not VCEP-approved)
- N581Y detected in WM3912 with predicted modest kinase activity (not a functional assay)
Still missing
- No VCEP-approved functional assay data (BRAF Kinase
- MEK Activation
- ERK Activation assays) for N581Y
Sources
PS4 No case-control data demonstrate an increased prevalence of N581Y in RASopathy-affected individuals versus controls. The variant has been reported in somatic cancers (COSMIC n=7) but not in germline RASopathy cohorts. Details ▾Hide ▴
Evidence considered
- N581Y reported in COSMIC (COSV56062673
- n=7 somatic observations)
- but no germline RASopathy proband data available
Still missing
- No RASopathy case counts for this variant
PM1 Per the RASopathy VCEP, PM1 is applicable only to specific critical and well-established functional domains: exon 6, exon 11, P-loop (AA 459-474), and CR3 activation segment (AA 594-627). N581 (position 581 in exon 14) lies outside these approved domains. Although the residue lies in a statistically significant hotspot, it does not qualify for PM1 under VCEP specifications. Details ▾Hide ▴
Evidence considered
- Residue N581 is in a statistically significant hotspot
- but not within VCEP-approved PM1 domains (P-loop 459-474
- CR3 activation segment 594-627)
PM5 PM5 requires a different pathogenic/likely pathogenic missense change at the same codon (N581). The pm5_candidates search found no qualifying comparator variants with established pathogenicity at codon 581 in BRAF. N581S and N581I have been reported in somatic cancers but none are established as germline pathogenic in the RASopathy context. Details ▾Hide ▴
Evidence considered
- No same-codon pathogenic/likely pathogenic missense comparators identified at N581
Still missing
- N581S and N581I reported somatically but lack germline pathogenic classification
Sources
pm5_candidates
PM6 No assumed de novo occurrence of N581Y has been reported. No proband data with unconfirmed parentage available. Details ▾Hide ▴
Still missing
- No de novo or assumed de novo reports
PP1 No co-segregation data available for N581Y in RASopathy families. No informative meioses reported. Details ▾Hide ▴
Still missing
- No family segregation data
BA1 BA1 requires gnomAD filtering allele frequency ≥0.05%. The variant is absent from all gnomAD populations (v2.1, v4.1, Canada). Details ▾Hide ▴
Evidence considered
- Absent from gnomAD v2.1 (0/0 allele count)
- Absent from gnomAD v4.1 (0/0 allele count)
Sources
BS1 BS1 requires gnomAD filtering allele frequency ≥0.025%. The variant is absent from all gnomAD populations. Details ▾Hide ▴
BS2 No evidence of N581Y observed in healthy adult individuals. The variant is absent from gnomAD, precluding any observation in presumed healthy controls. Details ▾Hide ▴
Still missing
- No healthy control observations
BS4 No segregation data available to demonstrate lack of segregation in affected family members. No informative meioses reported. Details ▾Hide ▴
Still missing
- No family segregation data for negative cosegregation
BP2 No evidence of an alternative molecular cause of a RASopathy in the same gene (in cis/trans with a pathogenic variant). No points-based scoring evidence available. Details ▾Hide ▴
Still missing
- No alternative molecular cause documented
BP4 BP4 requires REVEL ≤0.3 for missense variants per VCEP. The REVEL score for N581Y is 0.978, far exceeding the benign threshold. Multiple computational lines support a deleterious effect. Details ▾Hide ▴
Evidence considered
- REVEL = 0.978 (threshold ≤0.3 not met)
- BayesDel = 0.580
- SpliceAI max delta = 0.07 (no splicing impact)
Sources
BP5 No evidence of an alternative molecular cause of a RASopathy in a different gene, and no phenotype inconsistent with a RASopathy documented. Details ▾Hide ▴
Still missing
- No alternative molecular diagnosis documented
Not applicable · 8· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 VCEPPVS1 is not applicable per the ClinGen RASopathy VCEP v2.3.0 for BRAF. This is a missense variant (c.1741A>T, p.Asn581Tyr), not a null variant (nonsense, frameshift, or canonical splice site). Details ▾Hide ▴
No further detail was recorded.
PP4 VCEPPP4 is not applicable per the ClinGen RASopathy VCEP v2.3.0. The VCEP redirects phenotype specificity evaluation to PS4. Details ▾Hide ▴
No further detail was recorded.
PP5 VCEPPP5 is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee. Details ▾Hide ▴
No further detail was recorded.
BS3 VCEPBS3 is marked as not applicable in the ClinGen RASopathy VCEP v2.3.0 criteria for BRAF (all strength tiers listed as not applicable). Details ▾Hide ▴
No further detail was recorded.
BP1 N/ABP1 per the RASopathy VCEP is applicable only to truncating variants (nonsense, frameshift, canonical splice sites, initiation codon, or exon deletions) in genes where LOF is not an established disease mechanism. c.1741A>T is a missense variant and does not qualify. Details ▾Hide ▴
No further detail was recorded.
BP6 VCEPBP6 is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee. Details ▾Hide ▴
No further detail was recorded.
BP7 N/ABP7 applies only to synonymous (silent) variants or intronic positions outside canonical splice sites. c.1741A>T is a missense variant resulting in p.Asn581Tyr and does not qualify. Details ▾Hide ▴
No further detail was recorded.
PS5 N/APS5 is not a criterion in the ClinGen RASopathy VCEP v2.3.0 specification for BRAF. Details ▾Hide ▴
No further detail was recorded.
Identifiers
- Gene
- BRAF
- Transcript
- NM_004333.6
- Coding (HGVS c.)
- NM_004333.6:c.1741A>T
- Protein (HGVS p.)
- NP_004324.2:p.(Asn581Tyr)
- GRCh38
- chr7:140754187 T>A
- GRCh37
- chr7:140453987 T>A
- ClinVar
- 3257913
- COSMIC
- COSV56062673
Gene diagram
Every interpreted variant in BRAF, mapped onto the exon structure of NM_004333.6. Select a row to find it on the plot.
BRAFNM_004333.6
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 BRAF
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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
Allele count data not recorded
gnomAD v2.1
Allele count data not recorded
gnomAD-Canada v1.0
Allele count data not recorded
Statements
gnomAD v4.1
Absent from gnomAD v4.1.
gnomAD v2.1
Absent from gnomAD v2.1.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
SpliceAI and Pangolin
Other predictors
- REVEL
- 0.978
- BayesDel
- 0.580
How the predictions were used
PP3 SupportingREVEL score is 0.978, which meets the VCEP threshold of ≥0.7 for PP3 at Supporting strength. SpliceAI max delta score is 0.07, indicating no splicing impact that would contradict the disease mechanism. Details ▾Hide ▴
Evidence considered
- REVEL score = 0.978 (≥0.7 threshold)
- SpliceAI max delta = 0.07 (no predicted splicing impact)
Sources
revelspliceai ↗
BP4 BP4 requires REVEL ≤0.3 for missense variants per VCEP. The REVEL score for N581Y is 0.978, far exceeding the benign threshold. Multiple computational lines support a deleterious effect. Details ▾Hide ▴
Evidence considered
- REVEL = 0.978 (threshold ≤0.3 not met)
- BayesDel = 0.580
- SpliceAI max delta = 0.07 (no splicing impact)
Sources
BP7 N/ABP7 applies only to synonymous (silent) variants or intronic positions outside canonical splice sites. c.1741A>T is a missense variant resulting in p.Asn581Tyr and does not qualify. Details ▾Hide ▴
No further detail was recorded.
Statement
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.07). REVEL score = 0.978. BayesDel score = 0.579861.
6 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata.
Recorded publications
-
PMID 30224342 ↗Impact of BRAF Mutation Class on Disease Characteristics and Clinical Outcomes in BRAF-mutant Lung Cancer.Dagogo-Jack I et al. · 2019N581Y/S/I listed among BRAF mutations in a cohort of 236 NSCLC patients classified by functional class. N581Y was grouped within a list of class 2/3 mutations. No specific clinical or functional data were provided for N581Y.Names this variant
Quoted passage
G596R, D594Y/N/G/E, N581Y/S/I, G466V/L/E/A, D287Y
Figure 1/Table 1 (mutation classification list)
-
PMID 32540409 ↗Molecular Landscape of BRAF-Mutant NSCLC Reveals an Association Between Clonality and Driver Mutations and Identifies Targetable Non-V600 Driver Mutations.Negrao MV et al. · 2020BRAF N581Y identified as a novel activating mutation in Ba/F3 cell viability assays from a large cfDNA NSCLC cohort (Guardant360 database, n=1515 patients). N581Y was among 14 VUS tested; it and F468S were the two mutations found to be activating. N581Y was classified as clonal and associated with class 3 (RAS-dependent) BRAF signaling.Names this variant
Quoted passage
F468S and N581Y were identified as novel activating mutations.
Abstract; Results, 'Cell line models identify novel activating BRAF mutations'; Table 1; Figure 2
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PMID 19276360 ↗Antitumor efficacy of the novel RAF inhibitor GDC-0879 is predicted by BRAFV600E mutational status and sustained extracellular signal-regulated kinase/mitogen-activated protein kinase pathway suppression.Describes preclinical characterization of RAF inhibitor GDC-0879. Focused on BRAF V600E-mutant models. NM_004333.6:c.1741A>T (p.Asn581Tyr) was not mentioned.Does not name this variant
-
PMID 19474002 ↗Concomitant mutations and splice variants in KRAS and BRAF demonstrate complex perturbation of the Ras/Raf signalling pathway in advanced colorectal cancer.BRAF N581Y identified as a novel heterozygous mutation in colorectal cancer cell line HT55, located in exon 13 (kinase domain). The mutation was confirmed as expressed at the mRNA level. Both N581 and T529 are highly conserved residues.Names this variant
Quoted passage
HT55 had a N581Y mutation (fig 1b). Both of these mutations are situated in exon 13 and cause a change in conserved residues within the kinase domain of BRAF.
Results, BRAF mutation in cell lines; Table 1; Figure 1b
-
PMID 26084293 ↗ERBB activation modulates sensitivity to MEK1/2 inhibition in a subset of driver-negative melanoma.BRAF N581Y detected by MSKCC IMPACT assay in pan-negative melanoma cell line WM3912. The alteration was predicted to induce modest BRAF kinase activity but was poorly characterized. N581I was also detected in VP-Mel-21. N581-mutant cell lines spanned both Class I and Class II MEK inhibitor response phenotypes.Names this variant
Quoted passage
A non-canonical BRAF N581Y alteration was detected by IMPACT analysis in WM3912. This alteration is predicted to induce modest BRAF kinase activity, but is poorly characterized.
Results, 'Pan-negative melanomas display differential sensitivity to MEK1/2 inhibition'; Supplementary Table S6; 'ERBB and AKT activation status' section
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PMID 15035987 ↗Mechanism of activation of the RAF-ERK signaling pathway by oncogenic mutations of B-RAF.Wan PT et al. · 2004Characterized kinase activity of 22 B-RAF cancer mutants. N580S B-RAF (adjacent residue) was analyzed and found to have intermediate kinase activity. NM_004333.6:c.1741A>T (p.Asn581Tyr) was not among the mutants studied.Does not name this variant
Quoted passage
N580SB-RAF, and V599EB-RAF, whose in vitro basal kinase activities are between 1.3- and 480-fold higher than WTB-RAF activity
Results; Figure 1; Supplemental Table S1
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
gnomAD v4.1
Captured gnomAD v4.1 source record
Open source ↗
gnomAD v2.1
Captured gnomAD v2.1 source record
Open source ↗
SpliceAI Lookup
Recorded maximum delta 0.070
Open source ↗
ClinVar
Captured ClinVar source record
Open source ↗
COSMIC
Captured COSMIC source record
Open source ↗
Cancer hotspots
Captured Cancer Hotspots source record
Open source ↗
OncoKB
Captured OncoKB source record
Open source ↗
ClinGen CSpec
Captured ClinGen CSpec source record
Open source ↗
All source links
- ClinGen CSpec ↗cspec.genome.network/cspec/ui/svi/doc/643243119
- ClinVar ↗www.ncbi.nlm.nih.gov/clinvar/variation/3257913/
- gnomAD v2.1 ↗gnomad.broadinstitute.org/variant/7-140453987-T-A?dataset=gnomad_r2_1
- gnomAD v4.1 ↗gnomad.broadinstitute.org/variant/chr7-140754187-T-A?dataset=gn…
- gnomAD-Canada ↗http://192.168.4.76:8001/variant/7-140754187-T-A
- SpliceAI Lookup ↗spliceailookup.broadinstitute.org/#variant=NM_004333.6%3Ac.1741…
- OncoKB ↗www.oncokb.org/gene/BRAF/N581Y
- COSMIC ↗cancer.sanger.ac.uk/cosmic/mutation/overview?id=221423648
- Cancer hotspots ↗www.cancerhotspots.org/
Statements for reports
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
gnomAD v4.1
Absent from gnomAD v4.1.
gnomAD v2.1
Absent from gnomAD v2.1.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
ClinVar
This variant has been reported in ClinVar but submission details could not be extracted. (ClinVarID = 3257913)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.07). REVEL score = 0.978. BayesDel score = 0.579861.
Functional
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Gain-of-function; curated oncogenicity label: Likely Oncogenic.
Somatic
This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV56062673, n = 7 times).
Cancer Hotspots
This variant lies in a statistically significant hotspot.