rs1060500273

chr17-31230259-G-Achr17-31230259-G-Cchr17-31230259-G-T

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1_Moderate PM2 PP3_Strong PP5_Very_Strong

The NM_001042492.3(NF1):c.2991-1G>A variant causes a splice acceptor change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 2/2 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: NF1 NM_001042492.3 splice_acceptor
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:8
• Conservation: PhyloP100: 9.56

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]

ACMG classification

Verdict is Pathogenic. Variant got 16 ACMG points.

• PVS1: Splicing variant, NOT destroyed by nmd, known LOF gene, truncates exone, which is 0.0071596242 fraction of the gene. Cryptic splice site detected, with MaxEntScore 3.4, offset of 1, new splice context is: tgtttctatgtctatataAGtat. Cryptic site results in frameshift change. If cryptic site found is not functional and variant results in exon loss, it results in inframe change.
• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 17-31230259-G-A is Pathogenic according to our data. Variant chr17-31230259-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 404458.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-31230259-G-A is described in Lovd as [Pathogenic]. Variant chr17-31230259-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NF1	NM_001042492.3	c.2991-1G>A		splice_acceptor_variant		ENST00000358273.9
NF1	NM_000267.3	c.2991-1G>A		splice_acceptor_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NF1	ENST00000358273.9	c.2991-1G>A		splice_acceptor_variant		1	NM_001042492.3	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:8

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jan 18, 2021	Canonical splice site variant predicted to result in an in-frame deletion of exon 23, which would disrupt the critical GTPase activating protein domain (Xu 1990, Luo 2014); Deletions involving coding exons of this gene are a known mechanism of disease (Stenson 2014); Not observed in large population cohorts (Lek 2016); This variant is associated with the following publications: (PMID: 8829638, 18546366, 24357598, 10712197, 25525159) -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Aug 19, 2020	The NF1 c.2991-1G>A variant has been described in individuals affected with neurofibromatosis type 1 (NF1; Fahsold 2000, Perrin 1996). It is reported as pathogenic in ClinVar (Variation ID: 404458) and is absent from general population databases (1000 Genomes Project, Exome Variant Server, and Genome Aggregation Database), indicating it is not a common polymorphism. This variant abolishes the canonical splice acceptor site of intron 22, and experimental data demonstrates that this variant causes skipping of exon 23 in the mRNA transcript (Fahsold 2010, Perrin 1996). Skipping of exon 23 would result in the deletion of 41 amino acid residues, leaving the rest of the protein in-frame. Additionally, other variants at this nucleotide position (c.2991-1G>C, c.2991-1G>T) have been described in individuals with NF1 and are considered pathogenic (Fahsold 2010, Sabbagh 2013). Based on available information, the c.2991-1G>A variant is considered pathogenic. REFERENCES Fahsold R et al. Minor lesion mutational spectrum of the entire NF1 gene does not explain its high mutability but points to a functional domain upstream of the GAP-related domain. Am J Hum Genet. 2000 Mar;66(3):790-818. Perrin G et al. Two novel mutations affecting mRNA splicing of the neurofibromatosis type 1 (NF1) gene. Hum Mutat. 1996;7(2):172-5. Sabbagh A et al. NF1 molecular characterization and neurofibromatosis type I genotype-phenotype correlation: the French experience. Hum Mutat. 2013 Nov;34(11):1510-8. -
Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	May 09, 2018	- -

Neurofibromatosis, type 1 Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Sep 27, 2023	This sequence change affects an acceptor splice site in intron 22 of the NF1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in NF1 are known to be pathogenic (PMID: 10712197, 23913538). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individuals with neurofibromatosis type 1 (NF1) and/or neurofibromatosis-Noonan syndrome (PMID: 8829638, 10712197, 24357598). ClinVar contains an entry for this variant (Variation ID: 404458). Studies have shown that disruption of this splice site is associated with altered splicing resulting in an unknown protein product (PMID: 8829638, 10712197). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Mar 15, 2022	- -

Juvenile myelomonocytic leukemia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Dec 06, 2021

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Hereditary cancer-predisposing syndrome;CN230736:Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Apr 29, 2022

The c.2991-1G>A intronic pathogenic mutation results from a G to A substitution one nucleotide upstream from coding exon 23 of the NF1 gene. This alteration has been observed in multiple individuals with a diagnosis or clinical suspicion of neurofibromatosis type 1 and has been reported to cause abnormal splicing (Ekvall S et al. Am J Med Genet A, 2014 Mar;164A:579-87; Fahsold R et al. Am J Hum Genet, 2000 Mar;66:790-818; Perrin G et al. Hum Mutat, 1996;7:172-5; Pros E et al. Hum Mutat, 2008 Sep;29:E173-93). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site and will result in the creation or strengthening of a novel splice acceptor site. In addition to the clinical data presented in the literature, alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as a disease-causing mutation. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

research

Hauer Lab, Department Of Pediatric Oncology, Technical University Munich

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ACMG/AMP, PVS1, PM2, PP5 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.40	D
BayesDel_noAF	Pathogenic	0.34
Cadd	Pathogenic	35
Dann	Uncertain	0.99
Eigen	Pathogenic	1.2
Eigen_PC	Pathogenic	1.0
FATHMM_MKL	Pathogenic	0.99	D
MutationTaster	Benign	1.0	D;D
GERP RS		5.5

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.93
SpliceAI score (max)		1.0		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.87		Position offset: 2
DS_AL_spliceai		1.0		Position offset: 1

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

Publications

LitVar

Other links and lift over

dbSNP: rs1060500273; hg19: chr17-29557277;