NM_000267.3:c.2325+16C>G is an intronic variant located 16 bases downstream of NF1 exon 19. SpliceAI predicts no significant splicing impact (max delta score = 0.02), and the variant is not expected to alter neurofibromin function.1 This variant is observed at extremely low frequency in population databases: gnomAD v2.1 allele frequency 0.00497% (14/281,840 alleles) and gnomAD v4.1 allele frequency 0.01147% (185/1,612,866 alleles), with no homozygotes reported (PM2_Supporting).2 Multiple lines of computational evidence predict no deleterious effect: SpliceAI delta score of 0.02 indicates no significant splice alteration, and no protein-level consequence is predicted for this deep intronic change (BP4).3 This variant has been classified as Likely benign by 4 independent clinical diagnostic laboratories in ClinVar (VariationID: 512450), including GeneDx, Athena Diagnostics, Genome-Nilou Lab, and Labcorp Genetics (BP6).4 Applying the ACMG/AMP 2015 combination rules (PMID:25741868): 1 supporting pathogenic criterion (PM2_Supporting) and 2 supporting benign criteria (BP4, BP6). The preponderance of benign evidence supports classification as Likely Benign.5
NF1
Final classification
Likely Benign
NF1 c.2325+16C>G · p.?
NF1
NM_000267.3:c.2325+16C>G is an intronic variant located 16 bases downstream of NF1 exon 19. SpliceAI predicts no significant splicing impact (max delta score = 0.02), and the variant is not expected to alter neurofibromin function.
Neurofibromatosis and Schwannomatosis Specification v1.0.0 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, BP6 supporting; combination = 1 supporting + 2 supporting benign, which maps to Likely Benign.
Classification rationale
PM2
BP4BP6
Likely Benign
NF1 c.2325+16C>G
PM2 + BP4 + BP6
→
Likely Benign
Gene diagram
· NM_000267.3 · variants mapped to exon structure
NF1
NM_000267.3
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 16 assessed
Applied · 3
Strength
Supporting
Moderate
Strong
Very strong
✓
PM2
supporting
Pathogenic
NM_000267.3:c.2325+16C>G is observed at extremely low frequency in population databases: gnomAD v2.1 AF=0.00497% (14/281,840 alleles, 0 homozygotes) and gnomAD v4.1 AF=0.01147% (185/1,612,866 alleles, 0 homozygotes). Both frequencies are well below the 0.1% threshold.
gnomAD v2.1: AF=0.00497% (14/281840)gnomAD v4.1: AF=0.01147% (185/1
✓
BP4
supporting
Benign
Multiple lines of computational evidence suggest no impact on gene product. SpliceAI predicts no significant splicing alteration (max delta score = 0.02). REVEL and BayesDel scores are not available for this intronic variant, but the SpliceAI prediction is consistent with a benign interpretation.
SpliceAI max delta=0.02no predicted donor/acceptor gain or loss.
✓
BP6
supporting
Benign
NM_000267.3:c.2325+16C>G has been reported as Likely benign by 4 clinical testing laboratories in ClinVar (VariationID: 512450), including GeneDx, Athena Diagnostics, Genome-Nilou Lab, and Labcorp Genetics (formerly Invitae). All submissions are from reputable clinical diagnostic laboratories.
ClinVar: Likely benign (4 clinical laboratories — GeneDxAthena DiagnosticsGenome-Nilou Lab
Assessed · not applied
Pathogenic
PS2
No de novo occurrence data were identified for NM_000267.3:c.2325+16C>G in the available literature or ClinVar submissions.
PS3
No functional studies were identified for NM_000267.3:c.2325+16C>G.
PS4
No case-control or case-series data were identified for NM_000267.3:c.2325+16C>G.
PM1
The variant is not located in a known mutational hotspot or critical functional domain.
PM6
No confirmed de novo occurrence data were identified for NM_000267.3:c.2325+16C>G in ClinVar submissions or the available literature.
PP1
No segregation data are available for NM_000267.3:c.2325+16C>G in the literature or ClinVar submissions.
PP3
Multiple in silico tools do not support a deleterious effect.
PP4
No phenotype or family history data specific to NM_000267.3:c.2325+16C>G are available in the literature or ClinVar submissions.
PP5
ClinVar reports NM_000267.3:c.2325+16C>G as Likely benign by 4 clinical testing laboratories (GeneDx, Athena Diagnostics, Genome-Nilou Lab, Labcorp Genetics).
Benign
BA1
The highest population allele frequency is 0.01147% (gnomAD v4.1), well below the 1% threshold for BA1.
BS1
The highest population allele frequency is 0.01147% (gnomAD v4.1), which is below the 0.3% threshold for BS1.
BS2
No data are available regarding observation of NM_000267.3:c.2325+16C>G in healthy adults in the absence of NF1-related features.
BS3
No functional studies demonstrating a benign effect were identified for NM_000267.3:c.2325+16C>G.
BS4
No segregation data are available to evaluate lack of segregation with disease for NM_000267.3:c.2325+16C>G.
BP2
No data are available regarding observation of NM_000267.3:c.2325+16C>G in trans with a known pathogenic NF1 variant.
BP5
No data are available regarding an alternative molecular basis for disease in individuals carrying NM_000267.3:c.2325+16C>G.
N/A · 6
PVS1 · PS1 · PM5 · PP2 · BP1 · BP7
Research & evidence
Population frequency · supports benign
gnomAD v4.1
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 0.000114703; MAF= 0.01147%, 185/1612866 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 0.000154364; MAF= 0.01544%, 182/1179034 alleles, homozygotes = 0); grpmax FAF= 0.00013594.
v2.1
This variant is present in gnomAD v2.1 (AF= 4.96736e-05; MAF= 0.00497%, 14/281840 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 9.34507e-05; MAF= 0.00935%, 12/128410 alleles, homozygotes = 0); grpmax FAF= 5.412e-05.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.011%
· 185 / 1,612,866
0 hom · FAF 0.014%
0 hom · FAF 0.014%
European (non-Finnish) 182 / 1,179,034 |
0.015% |
African/African American 2 / 74,872 |
0.0027% |
Remaining individuals 1 / 62,438 |
0.0016% |
+ 7 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish)
gnomAD v2.1
0.005%
· 14 / 281,840
0 hom · FAF 0.0054%
0 hom · FAF 0.0054%
European (non-Finnish) 12 / 128,410 |
0.0093% |
African/African American 2 / 24,862 |
0.008% |
+ 6 not observed (Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
gnomAD Canada 🇨🇦
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
ClinVar
This variant has been reported in ClinVar as Likely benign (4 clinical laboratories). (ClinVarID = 512450)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02).
Functional
No data
No calibrated functional assay or RNA evidence was identified for this variant.
COSMIC
Somatic evidence
COSMIC
This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant cancer hotspot.
Sources & reference links
Triaged references · 8 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
26467025 ↗
A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.
CLINVAR
20065170 ↗
American Society of Clinical Oncology policy statement update: genetic and genomic testing for cancer susceptibility.
CLINVAR
26140447 ↗
Points to Consider: Ethical, Legal, and Psychosocial Implications of Genetic Testing in Children and Adolescents.
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