About NF1
No gene-level summary was recorded for this case.
Previous versions
Variant interpretation report
NF1 c.2355A>G, p.(Glu785=)
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 NF1 VCEP v1.0. 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: 1
Pathogenic criteria applied · 0
No pathogenic criterion marked as applied in the recorded assessment.
Benign criteria applied · 1
BP7Supporting
BP7 · supporting
NM_000267.3:c.2355A>G is a synonymous (silent) variant (p.Glu785=). SpliceAI predicts no impact on splicing with a maximum delta score of 0.00, indicating no effect on splice consensus sequences and no creation of a novel splice site. The variant is present in gnomAD in 38 alleles (v4.1), suggesting the nucleotide position is not highly conserved across the population. BP7 is met at supporting strength.
Recorded classification: Uncertain significance
ClinGen Neurofibromatosis and Schwannomatosis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for NF1 Version 1.0 v1.0 lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: BP7 supporting; combination = 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
38 / 1,613,806 alleles
gnomAD v4.1: 38 / 1,613,806 alleles. Recorded AF 2.35468e-05. Recorded homozygote count 0.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 1.41447e-05; MAF= 0.00141%, 4/282792 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.09698e-05; MAF= 0.00310%, 4/129158 alleles, homozygotes = 0); grpmax FAF= 7.01e-06.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
No listed criterion applied
SpliceAI score
0.000 maximum delta
Recorded SpliceAI maximum delta score: 0.000. Refer to the recorded PP3/BP4 rationale for interpretation.
ClinVar submissions
5 reported laboratory submissions
5 Likely benign. ClinVar API review status: criteria provided, multiple submitters, no conflicts.
Context only
ClinVar ↗
Functional evidence
Statement recorded
OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
No listed criterion applied
OncoKB ↗
COSMIC
Cancer Hotspots
Somatic evidence
No matching record reported
This variant has not previously been reported in somatic cancers (COSMIC).
Cancer Hotspots
This variant does not lie in a statistically significant hotspot.
Context only
For specialists
Technical detail
ACMG/AMP criteria under ClinGen NF1 VCEP v1.0, with the data and sources behind each one.
29 criteria with recorded statuses: 1 met · 19 not met · 0 not assessed · 9 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Met
Not met
Not assessed
Not applicable
NM_000267.3:c.2355A>G (p.Glu785=) is a synonymous variant in NF1 with no predicted splice impact (SpliceAI max delta 0.00).
The variant is present in gnomAD v2.1 at a frequency of 0.00141% (4/282,792 alleles) and in gnomAD v4.1 at 0.00235% (38/1,613,806 alleles), with no homozygotes observed.
ClinVar classifies this variant as Likely benign (Variation ID 230539) based on submissions from 5 clinical laboratories, with a review status of criteria provided, single submitter (1-star).
No publications directly mention or provide variant-specific evidence for NM_000267.3:c.2355A>G; literature review of available full-text articles (PMID: 25741868, 17636453, 25394175, 26324357) confirmed this variant is not cited in any publication.
BP7 is met at supporting strength: this synonymous variant is predicted to have no splice impact by SpliceAI and is present in population databases, consistent with a non-conserved, likely benign nucleotide position.
No pathogenic criteria are met. No benign criteria beyond BP7 are met. The ClinVar Likely benign classification is consistent with the evidence that this synonymous variant lacks functional consequence.
No criteria match.
Met · 1
BP7 SupportingNM_000267.3:c.2355A>G is a synonymous (silent) variant (p.Glu785=). SpliceAI predicts no impact on splicing with a maximum delta score of 0.00, indicating no effect on splice consensus sequences and no creation of a novel splice site. The variant is present in gnomAD in 38 alleles (v4.1), suggesting the nucleotide position is not highly conserved across the population. BP7 is met at supporting strength. Details ▾Hide ▴
Evidence considered
- Synonymous variant p.Glu785=
- SpliceAI max delta 0.00 predicts no splice impact
- present in gnomAD v2.1 (4 alleles) and v4.1 (38 alleles)
- consistent with a non-conserved nucleotide position
Still missing
- No direct phyloP or GERP conservation scores available to confirm nucleotide is not highly conserved
Sources
Not met · 19 · evaluated, threshold not reached
PS2 No de novo observations have been reported for NM_000267.3:c.2355A>G. No publications mention this specific variant. Details ▾Hide ▴
Evidence considered
- No de novo reports identified in ClinVar or literature
Still missing
- No trio or parent-of-origin data available
Sources
PS3 No functional studies have been performed on NM_000267.3:c.2355A>G (p.Glu785=). This synonymous variant has no predicted splice impact (SpliceAI delta 0.00), and no experimental functional data exist in the literature. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta 0.00
- no functional assays identified in literature
Still missing
- No in vitro or in vivo functional characterization of this variant
Sources
PS4 No case-control studies demonstrate enrichment of NM_000267.3:c.2355A>G in affected individuals. The variant has been observed in gnomAD in 4 (v2.1) to 38 (v4.1) alleles, inconsistent with a highly penetrant pathogenic variant. ClinVar lists the variant as Likely benign by 5 clinical laboratories, with no reports of the variant in affected individuals with NF1-specific phenotype. Details ▾Hide ▴
Evidence considered
- gnomAD v2.1: 4/282
- 792 alleles (0.00141%)
- gnomAD v4.1: 38/1
- 613
- 806 alleles (0.00235%)
- ClinVar Likely benign
- no case-level observations of affected status
Still missing
- No case-control association data
Sources
PM1 Although residue Glu785 falls within the cysteine-serine rich domain (CSD, residues ~543-909) of neurofibromin, this is a synonymous variant (p.Glu785=) with no predicted splice impact (SpliceAI delta 0.00). The amino acid sequence is unchanged, and the nucleotide substitution does not alter protein structure or function. Location in a functional domain does not confer pathogenic significance when the protein product is unaltered. Residue 785 is not a statistically significant hotspot (cancerhotspots.org). Details ▾Hide ▴
Evidence considered
- Position 785 in CSD domain but synonymous with no splice impact
- not a cancer hotspot residue
Sources
PM2 NM_000267.3:c.2355A>G is present in gnomAD v2.1 (4/282,792 alleles; AF 0.00141%) and gnomAD v4.1 (38/1,613,806 alleles; AF 0.00235%). Although the allele frequency is below the 0.1% threshold for dominant disorders, this is a synonymous variant with no predicted splice impact (SpliceAI delta 0.00). Population presence at any frequency in a synonymous variant without functional consequence does not support pathogenicity; rather, it is consistent with a benign polymorphism. PM2 is not appropriately applied to synonymous variants lacking functional evidence. Details ▾Hide ▴
Evidence considered
- gnomAD v2.1 AF 0.00141%
- gnomAD v4.1 AF 0.00235%
- synonymous variant with SpliceAI delta 0.00
Sources
PM6 No de novo observations have been reported for NM_000267.3:c.2355A>G. No publications mention this variant in the context of assumed de novo status. Details ▾Hide ▴
Evidence considered
- No de novo reports in ClinVar or literature
Still missing
- No trio data
- no parental testing data
Sources
PP1 No segregation data are available for NM_000267.3:c.2355A>G. No publications report cosegregation of this variant with NF1 in affected families. Details ▾Hide ▴
Evidence considered
- No segregation or family studies identified
Still missing
- No family segregation data available
Sources
PP3 In silico prediction tools do not support a deleterious effect for this synonymous variant. REVEL and BayesDel scores are not available for synonymous variants. SpliceAI predicts no splice impact (max delta 0.00). No computational evidence supports pathogenicity. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta 0.00
- REVEL/BayesDel not applicable to synonymous variants
Still missing
- No missense-specific in silico scores available for synonymous variants
Sources
PP4 No patient phenotype or family history data are available for this case. PP4 requires that the patient's phenotype is highly specific for NF1, which cannot be assessed without clinical information. Details ▾Hide ▴
Evidence considered
- No patient phenotype data provided in case materials
Still missing
- No clinical phenotype data available for the proband
PP5 ClinVar classifies NM_000267.3:c.2355A>G as Likely benign (Variation ID 230539, 5 clinical laboratories, review status: criteria provided, single submitter). PP5 requires a reputable source to report the variant as pathogenic; this variant is reported as benign/likely benign. PP5 is not met. Details ▾Hide ▴
Evidence considered
- ClinVar Likely benign classification
- 5 clinical labs
- 1-star review status
Sources
BA1 The maximum allele frequency of NM_000267.3:c.2355A>G in gnomAD is 0.00310% (gnomAD v2.1 NFE) and 0.00320% (gnomAD v4.1). This is well below the BA1 threshold of >1%. BA1 is not met. Details ▾Hide ▴
Evidence considered
- gnomAD v2.1 max AF 0.00310% (NFE)
- gnomAD v4.1 max AF 0.00320% (remaining)
- both well below 1% BA1 threshold
Sources
BS1 The maximum allele frequency of NM_000267.3:c.2355A>G in gnomAD is 0.00310% (gnomAD v2.1 NFE) and 0.00320% (gnomAD v4.1). This is well below the BS1 threshold of >0.3% for dominant disorders. BS1 is not met. Details ▾Hide ▴
Evidence considered
- gnomAD v2.1 max AF 0.00310%
- gnomAD v4.1 max AF 0.00320%
- both well below 0.3% BS1 threshold
Sources
BS2 No homozygotes are observed in gnomAD (0 homozygotes in both v2.1 and v4.1). No evidence exists of this variant being observed in a healthy adult individual in the absence of NF1. BS2 requires observation in a healthy adult without the disease, which is not documented here. Details ▾Hide ▴
Evidence considered
- No homozygotes in gnomAD
- gnomAD is a general population database
- not a confirmed healthy cohort
Still missing
- No explicit healthy adult carrier data with confirmed absence of NF1 features
Sources
BS3 No functional studies demonstrate that NM_000267.3:c.2355A>G has no damaging effect on protein function or splicing. While SpliceAI predicts no splice impact (delta 0.00), BS3 requires well-established functional studies showing no deleterious effect, which are not available. Details ▾Hide ▴
Evidence considered
- SpliceAI delta 0.00 suggests no splice impact
- but no dedicated functional assay has been performed
Still missing
- No in vitro functional studies (e.g.
- minigene splicing assay
- protein function assay) to confirm absence of effect
Sources
BS4 No segregation data are available to demonstrate lack of cosegregation of NM_000267.3:c.2355A>G with NF1. BS4 requires observation of non-segregation with disease in affected family members. Details ▾Hide ▴
Evidence considered
- No family segregation data available
Still missing
- No family studies or segregation data for this variant
Sources
BP2 No observation of NM_000267.3:c.2355A>G in trans with a known pathogenic NF1 variant has been reported. BP2 requires documentation of the variant occurring in trans with a pathogenic variant without clinical features of the disorder. Details ▾Hide ▴
Evidence considered
- No homozygous observations in gnomAD
- no reports of compound heterozygosity with pathogenic NF1 variants
Still missing
- No phasing data with known pathogenic NF1 variants
Sources
BP4 BP4 requires multiple lines of computational evidence suggesting no impact on the gene or gene product. Only SpliceAI is available for this synonymous variant (delta 0.00). REVEL and BayesDel are not applicable to synonymous variants. A single line of computational evidence is insufficient to meet BP4. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta 0.00 as sole in silico predictor
- REVEL/BayesDel/HCI not available for synonymous variants
Still missing
- No additional computational predictors (e.g.
- phyloP
- GERP
- CADD) available in case materials for this variant
Sources
BP5 No observation of NM_000267.3:c.2355A>G in a case where an alternate molecular basis for disease has been identified. BP5 requires documentation of the variant occurring in an individual with a different confirmed genetic etiology for NF1. Details ▾Hide ▴
Evidence considered
- No reports of co-occurrence with an alternate molecular diagnosis
Still missing
- No data on alternate molecular diagnoses in carriers of this variant
Sources
BP6 ClinVar classifies NM_000267.3:c.2355A>G as Likely benign (Variation ID 230539) with a review status of 'criteria provided, single submitter' (1-star). BP6 requires a reputable source to report the variant as benign with evidence unavailable for independent evaluation. While 5 clinical laboratories have submitted Likely benign classifications, the 1-star review status falls short of the 3-star expert panel threshold typically required for BP6 application under both VCEP and generic ACMG/AMP frameworks. Details ▾Hide ▴
Evidence considered
- ClinVar Likely benign
- 5 clinical labs
- 1-star review status
- no expert panel review
Still missing
- No expert panel (3-star) ClinVar review available
Sources
Not applicable · 9· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 N/ANM_000267.3:c.2355A>G is a synonymous variant (p.Glu785=) that does not result in a null allele (nonsense, frameshift, or canonical splice disruption). PVS1 is not applicable to synonymous variants. Details ▾Hide ▴
Evidence considered
- Synonymous variant (p.Glu785=)
- no predicted null effect on protein
Sources
pvs1_variant_assessment
PS1 N/APS1 applies when a different nucleotide change at the same position results in the same amino acid change as a known pathogenic variant. This is a synonymous variant with no amino acid change (p.Glu785=). PS1 is not applicable. Details ▾Hide ▴
Evidence considered
- Synonymous variant
- no amino acid change to compare
PM3 N/ASkipped per case instructions. PM3 applies to variants observed in trans with a pathogenic variant for recessive disorders; NF1 is autosomal dominant. Details ▾Hide ▴
No further detail was recorded.
PM4 N/ASkipped per case instructions. PM4 applies to in-frame deletions/insertions or stop-loss variants; NM_000267.3:c.2355A>G is a single-nucleotide synonymous substitution. Details ▾Hide ▴
No further detail was recorded.
PM5 N/ANM_000267.3:c.2355A>G is a synonymous variant (p.Glu785=). PM5 applies to missense variants at the same residue as a known pathogenic missense change. No amino acid change occurs; PM5 is not applicable. Details ▾Hide ▴
Evidence considered
- Synonymous variant
- pm5_candidates confirmed no classic same-residue PM5 semantics applicable
Sources
pm5_candidates
PP2 N/APP2 applies to missense variants in genes with a low rate of benign missense variation where missense variants are a common disease mechanism. NM_000267.3:c.2355A>G is a synonymous variant, not a missense change. PP2 is not applicable. Details ▾Hide ▴
Evidence considered
- Synonymous variant (p.Glu785=)
- not a missense change
BP1 N/ABP1 applies to missense variants in genes where truncating variants are the primary disease mechanism. NM_000267.3:c.2355A>G is a synonymous variant, not missense. BP1 is not applicable. Details ▾Hide ▴
Evidence considered
- Synonymous variant
- BP1 is specific to missense variants
BP3 N/ASkipped per case instructions. BP3 applies to in-frame deletions/insertions in repetitive regions; not applicable to a single-nucleotide synonymous substitution. Details ▾Hide ▴
No further detail was recorded.
PS5 N/APS5 applies when a different pathogenic missense change has been observed at the same amino acid residue. NM_000267.3:c.2355A>G is a synonymous variant (p.Glu785=) with no missense change. PS5 is not applicable. Details ▾Hide ▴
Evidence considered
- Synonymous variant
- no amino acid substitution to compare with known pathogenic missense variants
Identifiers
- Gene
- NF1
- Transcript
- NM_000267.3
- Coding (HGVS c.)
- NM_000267.3:c.2355A>G
- Protein (HGVS p.)
- NP_000258.1:p.(Glu785=)
- GRCh38
- chr17:31227552 A>G
- GRCh37
- chr17:29554570 A>G
- ClinVar
- 230539
Gene diagram
Every interpreted variant in NF1, mapped onto the exon structure of NM_000267.3. Select a row to find it on the plot.
NF1NM_000267.3
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 NF1
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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
38 / 1,613,806 alleles
AF 2.35e-05 · 0 homozygotes · FAF 2.23e-05
gnomAD v2.1
4 / 282,792 alleles
AF 1.41e-05 · 0 homozygotes · FAF 7.01e-06
gnomAD-Canada v1.0
Allele count data not recorded
By genetic ancestry
gnomAD v4.1
AF 2.4e-05 · 38 / 1,613,806 alleles · 0 hom · FAF 2.2e-05
| Remaining individuals2 / 62,466 | 3.2e-05 |
| European (non-Finnish)36 / 1,179,840 | 3.1e-05 |
0 alternate alleles recorded in 8 other groups: Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American.
gnomAD v2.1
AF 1.4e-05 · 4 / 282,792 alleles · 0 hom · FAF 7e-06
| European (non-Finnish)4 / 129,158 | 3.1e-05 |
0 alternate alleles recorded in 7 other groups: African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian.
Statements
gnomAD v4.1
This variant is present in gnomAD v4.1 (AF= 2.35468e-05; MAF= 0.00235%, 38/1613806 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 3.20174e-05; MAF= 0.00320%, 2/62466 alleles, homozygotes = 0); grpmax FAF= 2.234e-05.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 1.41447e-05; MAF= 0.00141%, 4/282792 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.09698e-05; MAF= 0.00310%, 4/129158 alleles, homozygotes = 0); grpmax FAF= 7.01e-06.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
SpliceAI and Pangolin
Other predictors
- REVEL
- Not available
- BayesDel
- Not available
How the predictions were used
BP7 SupportingNM_000267.3:c.2355A>G is a synonymous (silent) variant (p.Glu785=). SpliceAI predicts no impact on splicing with a maximum delta score of 0.00, indicating no effect on splice consensus sequences and no creation of a novel splice site. The variant is present in gnomAD in 38 alleles (v4.1), suggesting the nucleotide position is not highly conserved across the population. BP7 is met at supporting strength. Details ▾Hide ▴
Evidence considered
- Synonymous variant p.Glu785=
- SpliceAI max delta 0.00 predicts no splice impact
- present in gnomAD v2.1 (4 alleles) and v4.1 (38 alleles)
- consistent with a non-conserved nucleotide position
Still missing
- No direct phyloP or GERP conservation scores available to confirm nucleotide is not highly conserved
Sources
PP3 In silico prediction tools do not support a deleterious effect for this synonymous variant. REVEL and BayesDel scores are not available for synonymous variants. SpliceAI predicts no splice impact (max delta 0.00). No computational evidence supports pathogenicity. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta 0.00
- REVEL/BayesDel not applicable to synonymous variants
Still missing
- No missense-specific in silico scores available for synonymous variants
Sources
BP4 BP4 requires multiple lines of computational evidence suggesting no impact on the gene or gene product. Only SpliceAI is available for this synonymous variant (delta 0.00). REVEL and BayesDel are not applicable to synonymous variants. A single line of computational evidence is insufficient to meet BP4. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta 0.00 as sole in silico predictor
- REVEL/BayesDel/HCI not available for synonymous variants
Still missing
- No additional computational predictors (e.g.
- phyloP
- GERP
- CADD) available in case materials for this variant
Sources
Statement
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
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
-
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.Describes the ACMG/AMP standards and guidelines for interpretation of sequence variants. NM_000267.3:c.2355A>G was not identified in this paper.Does not name this variant
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PMID 17636453 ↗Neurofibromatosis type 1 in genetic counseling practice: recommendations of the National Society of Genetic Counselors.Radtke HB et al. · 2007Provides recommendations for genetic counseling of patients undergoing evaluation for or diagnosed with neurofibromatosis type 1. NM_000267.3:c.2355A>G was not identified in this paper.Does not name this variant
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PMID 25394175 ↗A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment.Hampel H et al. · 2015Presents referral indications for cancer predisposition assessment from ACMG and NSGC. NM_000267.3:c.2355A>G was not identified in this paper.Does not name this variant
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PMID 26324357 ↗American Society of Clinical Oncology Policy Statement Update: Genetic and Genomic Testing for Cancer Susceptibility.Robson ME et al. · 2015ASCO policy statement update on genetic and genomic testing for cancer susceptibility. NM_000267.3:c.2355A>G was not identified in this paper.Does not name this variant
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PMID 24893135 ↗Pheochromocytoma and paraganglioma: an endocrine society clinical practice guideline.Lenders JW et al. · 2014Pheochromocytoma and paraganglioma clinical practice guideline. No variant-specific content; paper was included in ClinVar submission context as background review. NM_000267.3:c.2355A>G was not identified.Does not name this variant
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PMID 28492532 ↗Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. General variant classification framework; NM_000267.3:c.2355A>G was not identified.Does not name this variant
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PMID 33939658 ↗The North American Neuroendocrine Tumor Society Consensus Guidelines for Surveillance and Management of Metastatic and/or Unresectable Pheochromocytoma and Paraganglioma.NANETS consensus guidelines for surveillance and management of pheochromocytoma and paraganglioma. NM_000267.3:c.2355A>G was not identified.Does not name this variant
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
gnomAD v4.1
38 / 1,613,806 recorded alleles
Open source ↗
gnomAD v2.1
Captured gnomAD v2.1 source record
Open source ↗
SpliceAI Lookup
Recorded maximum delta 0.000
Open source ↗
ClinVar
5 Likely benign
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/1553923915
- ClinVar ↗www.ncbi.nlm.nih.gov/clinvar/variation/230539/
- gnomAD v2.1 ↗gnomad.broadinstitute.org/variant/17-29554570-A-G?dataset=gnomad_r2_1
- gnomAD v4.1 ↗gnomad.broadinstitute.org/variant/chr17-31227552-A-G?dataset=gn…
- gnomAD-Canada ↗http://192.168.4.76:8001/variant/17-31227552-A-G
- SpliceAI Lookup ↗spliceailookup.broadinstitute.org/#variant=NM_000267.3%3Ac.2355…
- OncoKB ↗www.oncokb.org/gene/NF1/E785=
- COSMIC ↗cancer.sanger.ac.uk/cosmic/search?q=NF1+c.2355A%3EG
- 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
This variant is present in gnomAD v4.1 (AF= 2.35468e-05; MAF= 0.00235%, 38/1613806 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 3.20174e-05; MAF= 0.00320%, 2/62466 alleles, homozygotes = 0); grpmax FAF= 2.234e-05.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 1.41447e-05; MAF= 0.00141%, 4/282792 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.09698e-05; MAF= 0.00310%, 4/129158 alleles, homozygotes = 0); grpmax FAF= 7.01e-06.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
ClinVar
This variant has been reported in ClinVar as Likely benign (5 clinical laboratories). (ClinVarID = 230539)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
Functional
OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
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.