Variant classification summary

NM_000267.3:c.4270-9A>T

NF1 · NP_000258.1:p.? · NM_000267.3

GRCh37: chr17:29586041 A>T · GRCh38: chr17:31259023 A>T

Gene: NF1 Transcript: NM_000267.3

Final call

Likely Benign

PM2 supporting BP4 supporting BP6 supporting

Variant details

Gene

NF1

Transcript

NM_000267.3

Protein

NP_000258.1:p.?

gnomAD AF

4.539971203611223e-06 (v4.1)

ClinVar

Likely benign

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000267.3:c.4270-9A>T is an intronic substitution located at position -9 of the intron 32 splice acceptor site in NF1.

2

The variant is absent from gnomAD v2.1 and present at extremely low frequency in gnomAD v4.1 (7/1,541,860 alleles, AF = 0.00045%, no homozygotes), satisfying PM2_supporting.

3

SpliceAI predicts no splicing impact (max delta score = 0.00), supporting BP4_supporting.

4

A reputable clinical laboratory (Labcorp Genetics/Invitae) has classified this variant as Likely benign in ClinVar (Variation ID: 849602), satisfying BP6_supporting.

5

No pathogenic criteria were met. PVS1 is not applicable as the variant is outside canonical splice sites and SpliceAI predicts no impact. No de novo (PS2/PM6), functional (PS3/BS3), segregation (PP1/BS4), or case-control (PS4) evidence was identified for this variant.

6

With three supporting benign criteria (PM2_supporting, BP4_supporting, BP6_supporting) and no pathogenic criteria met, the variant is classified as Likely Benign per generic ACMG/AMP 2015 combination rules.

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 -9 of the intron 32 splice acceptor site. It does not fall into the canonical +/-1/2 splice consensus positions, and SpliceAI predicts no splicing impact (max delta = 0.00). The variant does not satisfy the generic ClinGen SVI PVS1 null-variant criteria (nonsense, frameshift, or canonical splice sites per PMC6185798).	spliceai pvs1_generic_framework
PS1	N/A	PS1 requires same amino acid change as an established pathogenic variant. This is an intronic variant with no predicted protein consequence (p.?). No same-residue comparator exists.
PS2	Not met	No de novo occurrence of NM_000267.3:c.4270-9A>T has been reported with confirmed paternity and maternity. De novo databases and ClinVar show no de novo assertions for this variant.
PS3	Not met	No well-established in vitro or in vivo functional studies have been identified that demonstrate a damaging effect of c.4270-9A>T on the gene or gene product. No minigene splicing assays, RNA studies, or protein functional data are available for this exact variant.
PS4	Not met	No case-control studies have demonstrated that the prevalence of c.4270-9A>T is significantly increased in affected individuals compared to controls. The variant is extremely rare in population databases (gnomAD v4.1 AF = 0.00045%), but this alone does not satisfy the case-control enrichment required for PS4.	gnomad_v4
PS5	N/A	PS5 applies when PM4/PM5 criteria are met but PS1/PS4 cannot be assessed. PM4/PM5 are not met for this intronic variant (no protein-level consequence comparator exists).
PM1	Not met	The variant is located in intron 32, not within a known mutational hotspot or critical functional domain of neurofibromin. PM1 requires location in a mutational hotspot and/or critical and well-established functional domain without benign variation.
PM2	Met	The variant is absent from gnomAD v2.1 and extremely rare in gnomAD v4.1 (7/1,541,860 alleles, AF = 4.54e-6, 0.00045%, all in European non-Finnish population, no homozygotes). The population frequency is well below the 0.1% threshold for PM2_supporting.	gnomad_v2 gnomad_v4
PM5	N/A	This is an intronic variant with no predicted missense amino acid consequence (p.?). No same-residue comparator variants exist for PM5 assessment. The pm5_candidates pipeline confirmed that the variant is ineligible for classic PM5 search.
PM6	Not met	No de novo observation (even without confirmation of paternity/maternity) has been reported for c.4270-9A>T in ClinVar, LOVD, or the published literature. No de novo assertions were identified for this variant.
PP1	Not met	No co-segregation data with disease in multiple affected family members has been reported for this variant. PP1 requires the variant to segregate with the phenotype in multiple affected family members across generations or in multiple affected siblings.
PP2	N/A	PP2 applies to missense variants in genes where missense variants are a common mechanism of disease and benign missense variation is rare. NF1 is a known loss-of-function gene, but this variant is intronic, not missense.
PP3	Not met	Multiple lines of computational evidence do not support a deleterious effect. SpliceAI predicts no splicing impact (max delta = 0.00). REVEL and BayesDel are not available for this intronic variant. No in silico tools predict a damaging consequence.	spliceai
PP4	Not met	The variant has been submitted to ClinVar by a single clinical laboratory, but the specific phenotype and clinical details of the proband are not available. PP4 requires that the variant is identified in an individual with a phenotype highly specific for the disease.	clinvar
PP5	Not met	The ClinVar classification for this variant is Likely benign (not pathogenic). The 12 PMIDs associated with the ClinVar entry are general clinical practice guidelines and review articles that do not mention the specific variant NM_000267.3:c.4270-9A>T. None of the cited publications contain variant-specific evidence to support a pathogenic assertion.	clinvar
BA1	Not met	The variant allele frequency in gnomAD v4.1 is 4.54e-6 (0.00045%), which is far below the BA1 threshold of greater than 1% (excludes benign standing in the population).	gnomad_v4
BS1	Not met	The variant allele frequency in gnomAD v4.1 is 4.54e-6 (0.00045%), which is below the BS1 threshold of greater than 0.3% (allele frequency greater than expected for disorder). The variant is too rare to support BS1.	gnomad_v4
BS2	Not met	BS2 requires observation of the variant in a healthy adult individual for a fully penetrant dominant disorder, or observation in trans with a pathogenic variant (in homozygous state) for a recessive disorder. No such observations are available for this variant. No homozygotes are reported in gnomAD.
BS3	Not met	No well-established in vitro or in vivo functional studies have been identified demonstrating that c.4270-9A>T does not alter splicing or protein function. BS3 requires functional evidence showing no damaging effect.
BS4	Not met	No evidence of lack of segregation has been reported. BS4 requires that the variant does not segregate with disease in affected members of a family. No family studies are available for this variant.
BP1	N/A	BP1 applies to missense variants in genes where truncating variants are the predominant mechanism of disease. This is an intronic variant (c.4270-9A>T), not a missense variant.
BP2	Not met	BP2 requires observation of the variant in trans with a pathogenic variant for a fully penetrant recessive disorder, or in cis with a pathogenic variant in any inheritance pattern. No such observations have been reported for c.4270-9A>T.
BP4	Met	Multiple lines of computational evidence suggest no impact on gene product. SpliceAI predicts no splicing alteration (max delta score = 0.00, with all four delta scores at 0.00: acceptor gain 0.00, acceptor loss 0.00, donor gain 0.00, donor loss 0.00). The variant is deep intronic and is not predicted to disrupt the native splice site.	spliceai
BP5	Not met	BP5 requires that the variant is found in a case with an alternate molecular basis for disease. No such observation has been reported for c.4270-9A>T.
BP6	Met	A reputable clinical testing laboratory (Labcorp Genetics, formerly Invitae) has classified this variant as Likely benign in ClinVar (Variation ID: 849602). Although the underlying evidence is not publicly available for independent evaluation, the classification from a clinical diagnostic laboratory with criteria provided supports a benign interpretation per BP6_supporting.	clinvar
BP7	N/A	BP7 applies to synonymous variants where splicing prediction algorithms predict no impact on the splice consensus sequence. This variant (c.4270-9A>T) is an intronic substitution, not a synonymous coding variant.

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