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NF1
Final classification
VUS
NF1 c.2355A>G · p.Glu785=
NF1

NM_000267.3:c.2355A>G (p.Glu785=) is a synonymous variant in NF1 with no predicted splice impact (SpliceAI max delta 0.00).

Gene
NF1
Transcript
NM_000267.3
HGVS · transcript:coding
NM_000267.3:c.2355A>G
Consequence
N/A
GRCh38
chr17:31227552 A>G
GRCh37
chr17:29554570 A>G
Basis 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.
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.
Classification rationale
BP7 VUS
NF1 c.2355A>G

NM_000267.3:c.2355A>G (p.Glu785=) is a synonymous variant in NF1 with no predicted splice impact (SpliceAI max delta 0.00).1 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.2 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).3 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.4 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.5 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.6

BP7 VUS
Gene diagram · NM_000267.3 · variants mapped to exon structure
NF1 NM_000267.3
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 19 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
BP7 supporting Benign
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.
Synonymous variant p.Glu785=SpliceAI max delta 0.00 predicts no splice impactpresent in gnomAD v2.1 (4 alleles) and v4.1 (38 alleles)
Assessed · not applied
Pathogenic
PS2 No de novo observations have been reported for NM_000267.3:c.2355A>G.
PS3 No functional studies have been performed on NM_000267.3:c.2355A>G (p.Glu785=).
PS4 No case-control studies demonstrate enrichment of NM_000267.3:c.2355A>G in affected individuals.
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).
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%).
PM6 No de novo observations have been reported for NM_000267.3:c.2355A>G.
PP1 No segregation data are available for NM_000267.3:c.2355A>G.
PP3 In silico prediction tools do not support a deleterious effect for this synonymous variant.
PP4 No patient phenotype or family history data are available for this case.
PP5 ClinVar classifies NM_000267.3:c.2355A>G as Likely benign (Variation ID 230539, 5 clinical laboratories, review status: criteria provided, single submitter).
Benign
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).
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).
BS2 No homozygotes are observed in gnomAD (0 homozygotes in both v2.1 and v4.1).
BS3 No functional studies demonstrate that NM_000267.3:c.2355A>G has no damaging effect on protein function or splicing.
BS4 No segregation data are available to demonstrate lack of cosegregation of NM_000267.3:c.2355A>G with NF1.
BP2 No observation of NM_000267.3:c.2355A>G in trans with a known pathogenic NF1 variant has been reported.
BP4 BP4 requires multiple lines of computational evidence suggesting no impact on the gene or gene product.
BP5 No observation of NM_000267.3:c.2355A>G in a case where an alternate molecular basis for disease has been identified.
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).
N/A · 8 PVS1 · PS1 · PM3 · PM4 · PM5 · PP2 · BP1 · BP3
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
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.
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.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.0024% · 38 / 1,613,806
0 hom · FAF 0.0022%
Remaining individuals
2 / 62,466
0.0032%
European (non-Finnish)
36 / 1,179,840
0.0031%
+ 8 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.0014% · 4 / 282,792
0 hom · FAF 0.0007%
European (non-Finnish)
4 / 129,158
0.0031%
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Likely benign (5 clinical laboratories). (ClinVarID = 230539)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 7 PMIDs not cited in assessment
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. CLINVAR
17636453 ↗ Neurofibromatosis type 1 in genetic counseling practice: recommendations of the National Society of Genetic Counselors. CLINVAR
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. CLINVAR
26324357 ↗ American Society of Clinical Oncology Policy Statement Update: Genetic and Genomic Testing for Cancer Susceptibility. CLINVAR
24893135 ↗ Pheochromocytoma and paraganglioma: an endocrine society clinical practice guideline. CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR
33939658 ↗ The North American Neuroendocrine Tumor Society Consensus Guidelines for Surveillance and Management of Metastatic and/or Unresectable Pheochromocytoma and Paraganglioma. CLINVAR