Variant classification summary

NM_000267.3:c.4661+11A>G

NF1 · NP_000258.1:p.? · NM_000267.3

GRCh37: chr17:29588886 A>G · GRCh38: chr17:31261868 A>G

Gene: NF1 Transcript: NM_000267.3

Final call

Likely Benign

BS3 supporting benign BP4 supporting benign BP6 supporting benign

Variant details

Gene

NF1

Transcript

NM_000267.3

Protein

NP_000258.1:p.?

gnomAD AF

0.0001742538400957466 (v4.1)

ClinVar

Likely benign

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000267.3:c.4661+11A>G is an intronic variant in NF1 (intron 34, +11 position) that has been observed in population databases at low frequency (gnomAD v2.1: 22/282,462 alleles, AF=0.0078%; v4.1: 281/1,612,590 alleles, AF=0.0174%).

2

Computational splicing prediction (SpliceAI, max delta = 0.10) indicates no significant impact on mRNA splicing.

3

A minigene splicing assay (Wimmer et al. 2007, PMID:17295913) demonstrated normal splicing of this variant with no exon skipping or cryptic splice site activation, providing functional evidence against a deleterious splicing effect (BS3_Supporting).

4

Multiple clinical laboratories in ClinVar classify this variant as Likely benign (4 of 7 usable submissions), with no pathogenic classifications reported (BP6_Supporting).

5

No pathogenic criteria are met. PVS1 is not applicable as this non-canonical intronic variant does not produce a null allele. PM2 is not met as the variant is present above absence thresholds. PS4 is not met due to population frequency inconsistent with a rare fully penetrant disorder. PS3 is not met as the only functional study shows normal splicing.

6

Based on the available evidence (BS3_Supporting, BP4_Supporting, BP6_Supporting), this variant meets criteria for Likely benign classification. Note: BS3 is from a single minigene assay requiring verification; BP4 is from SpliceAI computational prediction; BP6 is from ClinVar clinical laboratory consensus without expert panel review.

Final determination: Generic ACMG/AMP 2015 fallback rules support a Likely Benign classification because either one strong benign criterion plus one supporting benign criterion, or at least two supporting benign criteria, are present.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	This is an intronic variant at position +11, which does not fall into any null-variant bucket (nonsense, frameshift, or canonical ±1,2 splice consensus). The ClinGen SVI PVS1 decision tree does not apply to non-canonical intronic variants without demonstrated splicing aberration. A minigene assay demonstrated normal splicing (PMID:17295913), further confirming no null effect.	pvs1_variant_assessment pvs1_generic_framework
PS1	N/A	No amino acid change; intronic variant does not produce a missense alteration at a residue with a known pathogenic missense variant.
PS2	Not met	No confirmed de novo occurrence with maternity and paternity testing has been reported in the literature for this variant.
PS3	Not met	The only functional study identified (Wimmer et al. 2007, PMID:17295913) demonstrated normal splicing in a minigene assay, indicating no damaging effect on mRNA processing. No in vitro or in vivo studies have demonstrated a deleterious functional impact.
PS4	Not met	Although LOVD entries report multiple probands with NF1 carrying this variant, the variant is also observed in population databases at frequencies inconsistent with a fully penetrant rare disease allele (gnomAD v2.1: 22/282,462; v4.1: 281/1,612,590). The variant's prevalence in the general population precludes statistically significant enrichment in affected individuals.	gnomad_v2 gnomad_v4
PS5	N/A	No amino acid change; intronic variant does not create a missense change at a residue with a known pathogenic missense variant.
PM1	Not met	This intronic +11 position in intron 34 is not located in a well-established mutational hotspot or critical functional domain of NF1.
PM2	Not met	The variant is present in gnomAD at an allele frequency of 0.0078% (v2.1, 22/282,462 alleles) to 0.0174% (v4.1, 281/1,612,590 alleles), which exceeds the PM2 absence threshold (<0.1%) for a rare disease variant. The variant is observed across multiple subpopulations and in both exome and genome data.	gnomad_v2 gnomad_v4
PM5	N/A	No amino acid change; intronic variant has no residue context for same-residue comparator analysis. The pm5_candidates pipeline confirmed inability to parse missense residue context from the normalized protein consequence.	pm5_candidates
PM6	Not assessed	Exploratory search identified LOVD entries suggesting at least one apparently de novo occurrence without confirmed parentage. However, this could not be independently verified through the available case materials. Direct review of the LOVD database records is required before PM6 can be applied.
PP1	Not assessed	Exploratory search identified LOVD entries suggesting co-segregation in two small families. However, no published segregation analysis with statistical support was available for review. The variant is also observed in unaffected population controls, complicating segregation interpretation.
PP2	N/A	This is an intronic variant, not a missense variant. PP2 applies only to missense variants in genes with a low rate of benign missense variation.
PP3	Not met	SpliceAI predicts no significant splice impact (max delta score = 0.10). REVEL and BayesDel are not available for this intronic variant. No in silico tools support a deleterious effect on splicing.	spliceai
PP4	Not assessed	No patient-specific phenotypic data were provided with this case. Cannot assess whether the patient's phenotype or family history is highly specific for NF1.
PP5	Not met	No reputable source has recently reported this variant as pathogenic. ClinVar shows a consensus classification of Likely benign (4 clinical laboratories) and Uncertain significance (3 clinical laboratories). No ClinVar submission classifies this variant as pathogenic.	clinvar
BA1	Not met	The maximum allele frequency in gnomAD is 0.0227% (v4.1 European non-Finnish), which is well below the BA1 threshold of >1%.	gnomad_v2 gnomad_v4
BS1	Not met	The maximum allele frequency in gnomAD is 0.0227% (v4.1 European non-Finnish), which is below the BS1 threshold of >0.3%.	gnomad_v2 gnomad_v4
BS2	Not assessed	While the variant is observed in gnomAD at frequencies that suggest some carriers may be healthy adults (281 alleles in v4.1, with NF1 being nearly 100% penetrant by early childhood), gnomAD does not provide health status confirmation of carriers. Without documented observation in confirmed healthy adult individuals, BS2 cannot be formally applied.	gnomad_v2 gnomad_v4
BS3	Met	Wimmer et al. (2007) performed a minigene splicing assay demonstrating normal splicing of c.4661+11A>G with no exon skipping or cryptic splice site activation. This well-established functional assay provides evidence that the variant does not impair mRNA splicing, supporting a benign effect. Note: this finding was identified through exploratory analysis and should be verified by reviewing the full text of PMID:17295913.
BS4	Not assessed	Exploratory search identified a ClinVar submission (reportedly variation 428109) suggesting inheritance from an unaffected parent. However, this ClinVar variation ID differs from the primary variation for this variant (227742) and could not be independently verified. The submission provenance and the clinical certainty of the parent's unaffected status require direct review.
BP1	N/A	This is an intronic variant. BP1 applies specifically to missense variants in genes where a truncating mechanism causes disease.
BP2	Not met	No evidence of this variant occurring in trans with a known pathogenic NF1 variant has been reported. Given the autosomal dominant inheritance of NF1, such an observation would provide strong evidence for benignity but has not been documented.
BP3	N/A	Skipped — this is an intronic substitution, not an in-frame indel in a repetitive region.
BP4	Met	SpliceAI predicts no significant splice impact (max delta score = 0.10). REVEL and BayesDel are not applicable for this intronic variant. The available computational evidence does not support a deleterious splicing effect.	spliceai
BP5	Not met	No observation of this variant in a case where an alternative molecular basis for disease has been identified.
BP6	Met	Multiple clinical diagnostic laboratories (4 of 7 usable submissions) classify this variant as Likely benign in ClinVar. The majority consensus among clinical testing laboratories provides reputable source evidence supporting a benign interpretation.	clinvar
BP7	N/A	BP7 applies to synonymous variants with no predicted splice impact. This is an intronic variant at position +11, not a synonymous coding variant. While SpliceAI predicts no splice impact, the criterion is not directly applicable to deep intronic variants.

Disclaimer: The content and results provided by LYFE Sciences are for research and educational purposes only and must not be used as a substitute for professional medical judgment, diagnosis, or treatment. Always consult a qualified healthcare professional before making any clinical decisions.