NF1 p.Ile1402Ile

Variant names:

• chr17-31258376-C-A
• rs864622406
• NM_001042492.3:c.4206C>A
• NF1 p.Ile1402Ile

Your query was ambiguous. Multiple possible variants found:

• chr17-31258376-C-A
• chr17-31258376-C-T

GermlineCancer (beta)

Variant summary

Our verdict is Likely benign.

-2 Likely Benign

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received -2 classification points (ACGS-UK Somatic Oncogenicity v2025). O3_ModerateB4_Strong

The NM_001042492.3(NF1):c.4206C>A (p.Ile1402Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The gene NF1 is a tumor suppressor gene (CancerMine: 101 TSG, 30 oncogene, 95 driver citations). The gene NF1 is a known oncogene (CancerMine: 101 TSG, 30 oncogene, 95 driver citations). The gene NF1 is a cancer driver gene (CancerMine: 101 TSG, 30 oncogene, 95 driver citations). The variant is absent from the gnomAD population database at sites with sufficient sequencing coverage. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: NF1 NM_001042492.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182
• Publications: 0 publications found

Genes affected

NF1 (HGNC:7765): (neurofibromin 1) This gene product appears to function as a negative regulator of the ras signal transduction pathway. Mutations in this gene have been linked to neurofibromatosis type 1, juvenile myelomonocytic leukemia and Watson syndrome. The mRNA for this gene is subject to RNA editing (CGA>UGA->Arg1306Term) resulting in premature translation termination. Alternatively spliced transcript variants encoding different isoforms have also been described for this gene. [provided by RefSeq, Jul 2008]

NF1 Gene-Disease associations (from GenCC):

• neurofibromatosis type 1

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, ClinGen, G2P, Genomics England PanelApp
• neurofibromatosis-Noonan syndrome

  Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Genomics England PanelApp
• Moyamoya disease

  Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
• hereditary pheochromocytoma-paraganglioma

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• familial ovarian cancer

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: ClinGen

Classification according to ACGS-UK Somatic Oncogenicity v2025

Classification was made for transcript:

Our verdict: Likely_benign. The variant received -2 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	O3Absent or very rare in population		Absent or extremely rare in gnomAD (AC ≤ 2) — O3 moderate; GnomAD: AF = absent, AC = 0 — absent/extremely rare (O3 moderate [+2])
	B4Synonymous/intronic, no splicing impact		Synonymous/intronic variant with confirmed no splicing impact (B4 strong); Synonymous variant — splicing algorithms confirm no impact on splicing (B4 strong [-4])

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_001042492.3. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	NF1 NM_001042492.3	MANE Select	c.4206C>A p.Ile1402Ile	synonymous	Exon 32 of 58	Prot: NP_001035957.1 UniProt:
	NF1 NM_000267.4		c.4143C>A p.Ile1381Ile	synonymous	Exon 31 of 57	Prot: NP_000258.1 UniProt:

NF1 NM_001042492.3

MANE Select

HGVSc / HGVSpc.4206C>Ap.Ile1402Ile

Exon rankExon 32 of 58

synonymous

Prot: NP_001035957.1UniProt: P21359-1

NF1 NM_000267.4

HGVSc / HGVSpc.4143C>Ap.Ile1381Ile

Exon rankExon 31 of 57

synonymous

Prot: NP_000258.1UniProt: P21359-2

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	NF1 ENST00000358273.9	TSL:1MANE Select	c.4206C>A p.Ile1402Ile	synonymous	Exon 32 of 58	Prot: ENSP00000351015.4 UniProt:
	NF1 ENST00000356175.7	TSL:1	c.4143C>A p.Ile1381Ile	synonymous	Exon 31 of 57	Prot: ENSP00000348498.3 UniProt:
	NF1 ENST00000579081.6	TSL:1	n.4143C>A	non_coding_transcript_exon	Exon 31 of 58	Prot: ENSP00000462408.2 UniProt:

NF1 ENST00000358273.9

TSL:1MANE Select

HGVSc / HGVSpc.4206C>Ap.Ile1402Ile

Exon rankExon 32 of 58

synonymous

Prot: ENSP00000351015.4UniProt: P21359-1

NF1 ENST00000356175.7

TSL:1

HGVSc / HGVSpc.4143C>Ap.Ile1381Ile

Exon rankExon 31 of 57

synonymous

Prot: ENSP00000348498.3UniProt: P21359-2

NF1 ENST00000579081.6

TSL:1

HGVSc / HGVSpn.4143C>A

Exon rankExon 31 of 58

non_coding_transcript_exon

Prot: ENSP00000462408.2UniProt: J3KSB5

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 3 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:32
GnomAD4 exome	AF:	AC:	Hom:	AN:	Cov:31
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:32

Showing 3 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Pathogenic	21
BayesDel_noAF	Benign	-0.17
CADD	Benign	7.2
DANN	Benign	0.74
GPN-Star LLR	N/A	-6.6
GPN-Star score	N/A	6.6
PhyloP100	Benign	0.18
RBP_binding_hub_radar	N/A	0.0
RBP_regulation_power_radar	N/A	1.7

Showing 9 of 9 scores

Splicing Scores

Algorithm	Calibrated pred.	Score	Prediction
Pangolin (max)	Benign	0.090
SpliceAI score (max)	Benign	0.10	Details are displayed if max score is > 0.2

Showing 2 of 2 scores

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Other links and lift over

dbSNP: rs864622406;

hg19: chr17-29585394;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar