rs267606606

chr17-31229953-CAAT-C

Variant summary

Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PM1 PM2 PM4_Supporting PP5_Very_Strong

The NM_001042492.3(NF1):c.2970_2972del(p.Met992del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000343 in 1,459,504 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000034 (0 hom.)
• Consequence: NF1 NM_001042492.3 inframe_deletion
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:23 O:1
• Conservation: PhyloP100: 8.91

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 13 ACMG points.

• PM1: In a hotspot region, there are 4 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 14 uncertain in NM_001042492.3
• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in NM_001042492.3. Strenght limited to Supporting due to length of the change: 1aa.
• PP5: Variant 17-31229953-CAAT-C is Pathogenic according to our data. Variant chr17-31229953-CAAT-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 363.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-31229953-CAAT-C is described in Lovd as [Pathogenic]. Variant chr17-31229953-CAAT-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NF1	NM_001042492.3	c.2970_2972del	p.Met992del	inframe_deletion	22/58	ENST00000358273.9
NF1	NM_000267.3	c.2970_2972del	p.Met992del	inframe_deletion	22/57

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NF1	ENST00000358273.9	c.2970_2972del	p.Met992del	inframe_deletion	22/58	1	NM_001042492.3	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000399 AC: 1 AN: 250346 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 135546

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000884

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000343 AC: 5 AN: 1459504 Hom.: 0 AF XY: 0.00000413 AC XY: 3 AN XY: 726064

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000187

Gnomad4 NFE exome AF: 0.00000270

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:23 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Neurofibromatosis, type 1 Pathogenic:10 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Dec 15, 2016	The p.Met992del variant in NF1 has been previously reported in >20 individuals w ith NF1, segregated with disease in >20 affected relatives, and was de novo in a t least 1 of these individuals (Upadhyaya 2007, Quintans 2011). Individuals with this variant were reported to not have cutaneous neurofibromas (Upadhyaya 2007, Quintans 2011). This variant has also been reported in ClinVar (Variation ID: 3 63) and has been identified in 1/66338 European chromosomes by the Exome Aggrega tion Consortium (ExAC, http://exac.broadinstitute.org). This variant is a deleti on of 1 amino acid at position 992 and is not predicted to alter the protein rea ding frame. In summary, this variant meets our criteria to be classified as path ogenic for NF1 in an autosomal dominant manner based upon frequency in probands and segregation studies. -
Pathogenic, criteria provided, single submitter	clinical testing	Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	May 08, 2023	PS4, PM2, PM4, PM6_Strong, PP1_Strong -
Pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Nov 09, 2021	- -
not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Center for Human Genetics, Inc, Center for Human Genetics, Inc	Nov 01, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Feb 24, 2020	Variant summary: NF1 c.2970_2972delAAT (p.Met992del) results in an in-frame deletion that is predicted to remove one amino acid from the encoded protein. The variant allele was found at a frequency of 4e-06 in 250346 control chromosomes. c.2970_2972delAAT has been reported in the literature in a large number of individuals affected with NF1 Related Conditions (e.g. Stevenson_2006, Tsipi_2018, Koczkowska_2019). These data indicate that the variant is very likely to be associated with disease. A study on 135 individuals carrying this variant showed that these individuals have a mild NF1 phenotype lacking clinically suspected plexiform, cutaneous, or subcutaneous neurofibromas (Koczkowska_2019). Six clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Nov 24, 2023	This variant, c.2970_2972del, results in the deletion of 1 amino acid(s) of the NF1 protein (p.Met992del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs267606606, gnomAD no frequency). This variant has been observed in individual(s) with clinical features of NF1-related conditions (PMID: 7904209, 12807981, 17160901, 20602485, 21532985, 23047742). In at least one individual the variant was observed to be de novo. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 363). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Mar 15, 2022	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics, University of Zurich	May 10, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	3billion	May 22, 2022	The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: <0.001%). Inframe deletion located in a nonrepeat region: predicted to change the length of the protein and disrupt normal protein function. The variant has been previously reported as de novo in a similarly affected individual (PMID: 30190611) and observed in multiple (>3) similarly affected unrelated individuals (PMID:23656349, 30190611, 30308447). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -
Pathogenic, criteria provided, single submitter	clinical testing	Medical Genetics, University of Parma	Dec 20, 2019	- -

not provided Pathogenic:7

Pathogenic, criteria provided, single submitter	clinical testing	Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes	Jan 16, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Jan 06, 2021	The NF1 c.2970_2972delAAT; p.Met992del variant (rs267606606) is reported in the literature in several unrelated individuals and families affected with a milder form of neurofibromatosis type 1 (NF1), characterized by a lack of neurofibromas (Kehrer-Sawatzki 2015, Koczkowska 2019, Quintans 2011, Upadhyaya 2007). This variant is also reported in ClinVar (Variation ID: 363). This variant is only observed on one allele in the Genome Aggregation Database, indicating it is not a common polymorphism. This variant deletes a single methionine residue leaving the rest of the protein in-frame. Based on available information, information, this variant is considered to be pathogenic. References: Kehrer-Sawatzki H et al. Neurofibromatosis Type 1 Without Neurofibromas: Genotype-Phenotype Correlations in NF1. Hum Mutat. 2015 Nov;36(11):v. Koczkowska M et al. Expanding the clinical phenotype of individuals with a 3-bp in-frame deletion of the NF1 gene (c.2970_2972del): an update of genotype-phenotype correlation. Genet Med. 2019 Apr;21(4):867-876. Quintans B et al. Neurofibromatosis without Neurofibromas: Confirmation of a Genotype-Phenotype Correlation and Implications for Genetic Testing. Case Rep Neurol. 2011 Apr 11;3(1):86-90. Upadhyaya M et al. An absence of cutaneous neurofibromas associated with a 3-bp inframe deletion in exon 17 of the NF1 gene (c.2970-2972 delAAT): evidence of a clinically significant NF1 genotype-phenotype correlation. Am J Hum Genet. 2007 Jan;80(1):140-51. -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Nov 22, 2019	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jan 05, 2022	In-frame deletion of 1 amino acid in a non-repeat region; In silico analysis supports a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 26740943, 26056819, 25329635, 26345759, 12807981, 25074460, 26962827, 27920686, 28213670, 27785414, 27322453, 10712197, 10862084, 7904209, 14569132, 16380919, 16542390, 20602485, 23047742, 26457592, 25966637, 16944272, 18546366, 23656349, 25370043, 23972508, 17160901, 26178382, 24232412, 26979265, 26956402, 27838393, 30190611, 30109123, 1568246, 29968256, 31717729, 31776437, 21532985, 31370276, 32107864, 25486365, 2121369) -
Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Nov 23, 2022	PP1_strong, PM2, PM6, PS4_moderate -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Oct 01, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	Oct 23, 2020	- -

Neurofibromatosis, type 1;C0349639:Juvenile myelomonocytic leukemia;C0553586:Café-au-lait macules with pulmonary stenosis;C1834235:Neurofibromatosis, familial spinal;C2931482:Neurofibromatosis-Noonan syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Sep 28, 2021

- -

Neurofibromatosis-Noonan syndrome Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jan 01, 2007

- -

Juvenile myelomonocytic leukemia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Sep 26, 2021

- -

Gastric cancer Pathogenic:1

Pathogenic, no assertion criteria provided

research

Laboratory for Genotyping Development, RIKEN

Jul 01, 2021

- -

Café-au-lait macules with pulmonary stenosis Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jan 01, 2007

- -

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jan 19, 2015

​The c.2970_2972delAAT pathogenic mutation (also known as p.M992del and delM992) is located in coding exon 22 of the NF1 gene. This alteration results from an in-frame AAT deletion between nucleotide positions 2970 and 2972. This results in the deletion of a highly conserved methionine residue at codon992. This alteration was first identified in two unrelated probands with paternally inherited neurofibromatosis type 1 (NF1) (Shen MH et al. Hum Mol Genet. 1993; 2(11):1861-4). Later studies suggest this mutation is associated with an attenuated form of NF1 similar to Legious syndrome; individuals with this mutation are not likely to develop neurofibromas (Upadhyaya M et al. Am J Hum Genet. 2007; 80(1):140-51). Based on the supporting evidence, c.2970_2972delAAT is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs267606606; hg19: chr17-29556971;