NM_000267.3:c.2325+16C>G

NF1 · NP_000258.1:p.? · NM_000267.3

GRCh37: chr17:29554325 C>G · GRCh38: chr17:31227307 C>G

Gene: NF1 Transcript: NM_000267.3

Final call

Likely Benign

BP4 supporting benign BP6 supporting benign

Variant details

Gene

NF1

Transcript

NM_000267.3

Protein

NP_000258.1:p.?

gnomAD AF

0.00011470264733710054 (v4.1)

ClinVar

Likely benign

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_000267.3:c.2325+16C>G is an intronic variant located at position +16 in intron 19 of NF1. SpliceAI predicts no splicing impact (max delta score 0.02).

This variant is present in gnomAD population databases at very low frequency: 14 of 281,840 alleles in v2.1 (AF=0.005%) and 185 of 1,612,866 alleles in v4.1 (AF=0.011%). It is absent from gnomAD-Canada.

In ClinVar, this variant is classified as Likely benign (VariationID 512450) by 4 clinical laboratories including GeneDx, Athena Diagnostics, Genome-Nilou Lab, and Labcorp Genetics.

No published literature was identified that directly mentions NM_000267.3:c.2325+16C>G. Eight papers from the ClinVar submission record were reviewed; all are general guidelines, methodology papers, or disease reviews that do not report this specific variant.

The available evidence supports a likely benign interpretation: BP4 (SpliceAI predicts no splicing impact) and BP6 (ClinVar consensus of Likely benign from 4 clinical laboratories). No pathogenic criteria are met.

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	Intronic variant at +16 position (intron 19), outside the canonical splice donor/acceptor consensus sites. SpliceAI max delta score is 0.02, confirming no predicted splicing impact. Does not meet PVS1 null-variant criteria per ClinGen SVI PVS1 framework (PMC6185798).	spliceai pvs1_generic_framework
PS1	N/A	Intronic variant with no protein amino acid consequence; cannot be compared to known pathogenic missense changes at the same residue.
PS2	Not assessed	No de novo observations for this variant were identified in ClinVar, the literature, or any other source.
PS3	Not assessed	No variant-specific in vitro or in vivo functional studies were identified. None of the reviewed publications contain functional data for NM_000267.3:c.2325+16C>G.
PS4	Not assessed	No case-control studies or statistical prevalence data comparing affected individuals to population controls were identified for this variant.
PS5	Not assessed	No VCEP/CSPEC definition of PS5 is available for NF1; the generic ACMG/AMP 2015 framework does not include PS5. No functional or phenotype-specific evidence was identified.
PM1	Not met	This intronic variant at +16 of intron 19 is not located in a well-established functional domain or recognized mutational hotspot within NF1.
PM2	Not met	This variant is observed in gnomAD population databases (14 alleles in v2.1, 185 alleles in v4.1), which does not satisfy the PM2 requirement of absence from controls for a fully penetrant autosomal dominant disorder. Although allele frequency is below the 0.1% threshold (v2.1: 0.005%, v4.1: 0.011%), the presence of any alleles in population cohorts contraindicates PM2 for NF1.	gnomad_v2 gnomad_v4
PM5	N/A	Intronic variant with no amino acid change; cannot compare to pathogenic missense changes at the same residue.
PM6	Not assessed	No de novo observations (assumed or confirmed) were identified for this variant in any source.
PP1	Not assessed	No segregation data are available for this variant in any reviewed source.
PP2	N/A	Intronic variant, not a missense change. PP2 applies only to missense variants in genes with a low rate of benign missense variation.
PP3	Not met	SpliceAI predicts no splicing impact (max delta score = 0.02). No REVEL, BayesDel, or HCI prior scores are available for this intronic variant. In silico evidence does not support a deleterious effect.	spliceai
PP4	Not assessed	No patient phenotype or clinical data are available for assessment. The variant has been reported in ClinVar as Likely benign but without detailed phenotypic information.
PP5	Not met	This variant is classified as Likely benign in ClinVar (VariationID 512450) by 4 clinical laboratories, not as pathogenic. PP5 requires a reputable source to have reported the variant as pathogenic.	clinvar
BA1	Not met	The maximum observed allele frequency is 0.011% (gnomAD v4.1), far below the 1% threshold for BA1.	gnomad_v2 gnomad_v4
BS1	Not met	The maximum observed allele frequency is 0.011% (gnomAD v4.1), far below the 0.3% threshold for BS1.	gnomad_v2 gnomad_v4
BS2	Not assessed	While this variant is observed in gnomAD (185 alleles in v4.1, 14 in v2.1), individual-level phenotype data are not available to confirm that these carriers are unaffected healthy adults. BS2 cannot be applied without individual phenotype confirmation.	gnomad_v2 gnomad_v4
BS3	Not met	No variant-specific well-established in vitro or in vivo functional studies demonstrating no damaging effect were identified. SpliceAI is an in silico predictor and does not qualify as a functional study under BS3.
BS4	Not assessed	No segregation data are available to evaluate lack of segregation with disease in affected families.
BP1	N/A	Intronic variant, not a missense change. BP1 applies only to missense variants in genes where truncating variants are the primary disease mechanism.
BP2	Not assessed	No phasing data are available to determine whether this variant has been observed in trans with a known pathogenic NF1 variant.
BP4	Met	SpliceAI predicts no splicing impact with a maximum delta score of 0.02, indicating this intronic variant is unlikely to alter splicing. No other in silico predictors suggest a deleterious effect.	spliceai
BP5	Not assessed	No data are available indicating this variant has been identified in a case where an alternative molecular basis for disease has been established.
BP6	Met	This variant is classified as Likely benign in ClinVar (VariationID 512450) by 4 clinical testing laboratories including GeneDx, Athena Diagnostics, Labcorp Genetics (formerly Invitae), and Genome-Nilou Lab. Although review status is criteria provided, single submitter per submission, the consistent classification across multiple independent laboratories supports a benign interpretation.	clinvar
BP7	N/A	Intronic variant at +16 position, not a synonymous (silent) coding change. BP7 applies only to synonymous variants with no predicted splicing impact.

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.