Variant classification summary

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

PM2 supporting BP4 supporting BP6 supporting

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

1

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.

2

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).

3

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).

4

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).

5

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.

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	NM_000267.3:c.2325+16C>G is an intronic variant located 16 bases downstream of exon 19. It does not fall into the generic PVS1 null-variant buckets of nonsense, frameshift, or canonical ±1,2 splice consensus variants, and the ClinGen SVI PVS1 framework (PMC6185798) does not apply.	pvs1_variant_assessment
PS1	N/A	PS1 applies when a variant produces the same amino acid change as a known pathogenic variant. NM_000267.3:c.2325+16C>G is intronic and does not alter the protein coding sequence.
PS2	Not assessed	No de novo occurrence data were identified for NM_000267.3:c.2325+16C>G in the available literature or ClinVar submissions.
PS3	Not assessed	No functional studies were identified for NM_000267.3:c.2325+16C>G. The three full-text publications reviewed (PMID:25741868, PMID:26467025, PMID:20065170) do not mention this variant, and no other functional data are available.
PS4	Not assessed	No case-control or case-series data were identified for NM_000267.3:c.2325+16C>G. The variant is present in gnomAD at low frequency and has been observed in clinical testing but without case-level detail.
PS5	N/A	PS5 applies to missense variants at a residue where a different missense change is known to be pathogenic. NM_000267.3:c.2325+16C>G is intronic and does not alter the protein coding sequence.
PM1	Not met	The variant is not located in a known mutational hotspot or critical functional domain. Hotspot analysis shows residue_significant=false and exact_variant_listed=no.
PM2	Met	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 gnomad_v4
PM5	N/A	Unable to confirm classic same-residue PM5 semantics. The variant is intronic and does not produce a missense change; no residue context can be determined for comparator analysis.	pm5_candidates
PM6	Not assessed	No confirmed de novo occurrence data were identified for NM_000267.3:c.2325+16C>G in ClinVar submissions or the available literature.
PP1	Not assessed	No segregation data are available for NM_000267.3:c.2325+16C>G in the literature or ClinVar submissions.
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. NM_000267.3:c.2325+16C>G is intronic and not a missense change.
PP3	Not met	Multiple in silico tools do not support a deleterious effect. SpliceAI predicts no significant splice impact (max delta score = 0.02). REVEL and BayesDel scores are not available for this intronic variant. HCI prior is not available for NF1.	spliceai
PP4	Not assessed	No phenotype or family history data specific to NM_000267.3:c.2325+16C>G are available in the literature or ClinVar submissions.
PP5	Not met	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). No reputable source reports this variant as pathogenic.	clinvar
BA1	Not met	The highest population allele frequency is 0.01147% (gnomAD v4.1), well below the 1% threshold for BA1.	gnomad_v2 gnomad_v4
BS1	Not met	The highest population allele frequency is 0.01147% (gnomAD v4.1), which is below the 0.3% threshold for BS1.	gnomad_v2 gnomad_v4
BS2	Not assessed	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	Not assessed	No functional studies demonstrating a benign effect were identified for NM_000267.3:c.2325+16C>G. The SpliceAI delta score of 0.02 suggests no splicing impact but is assessed under BP4 rather than BS3.
BS4	Not assessed	No segregation data are available to evaluate lack of segregation with disease for NM_000267.3:c.2325+16C>G.
BP1	N/A	BP1 applies to missense variants in genes where a truncating mechanism is predominant. NM_000267.3:c.2325+16C>G is intronic and not a missense change.
BP2	Not assessed	No data are available regarding observation of NM_000267.3:c.2325+16C>G in trans with a known pathogenic NF1 variant.
BP4	Met	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
BP5	Not assessed	No data are available regarding an alternative molecular basis for disease in individuals carrying NM_000267.3:c.2325+16C>G.
BP6	Met	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
BP7	N/A	BP7 applies to synonymous variants with no predicted splice impact. NM_000267.3:c.2325+16C>G is an intronic variant, not a synonymous coding change.

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