17-31221932-A-G

Position:

• chr17-31221932-A-G

Variant summary

Our verdict is Pathogenic. Variant got 15 ACMG points: 15P and 0B. PM1 PM2 PM5 PP2 PP5_Very_Strong

The NM_001128147.3(NF1):​c.1724A>G​(p.Tyr575Cys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y575H) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: NF1 NM_001128147.3 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:15
• Conservation: PhyloP100: 6.61

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 15 ACMG points.

• PM1: In a helix (size 19) in uniprot entity NF1_HUMAN there are 11 pathogenic changes around while only 1 benign (92%) in NM_001128147.3
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr17-31221931-T-C is described in Lovd as [Pathogenic].
• PP2: Missense variant in gene, where missense usually causes diseases (based on misZ statistic), NF1. . Gene score misZ 6.5427 (greater than the threshold 3.09). Trascript score misZ 3.8681 (greater than threshold 3.09). GenCC has associacion of gene with neurofibromatosis, familial spinal, hereditary pheochromocytoma-paraganglioma, neurofibromatosis type 1, Watson syndrome, neurofibromatosis-Noonan syndrome, Moyamoya disease, familial ovarian cancer.
• PP5: Variant 17-31221932-A-G is Pathogenic according to our data. Variant chr17-31221932-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 374108.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-31221932-A-G is described in Lovd as [Pathogenic]. Variant chr17-31221932-A-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NF1	NM_001042492.3	c.1721+3A>G		splice_region_variant, intron_variant		ENST00000358273.9	NP_001035957.1
NF1	NM_001128147.3	c.1724A>G	p.Tyr575Cys	missense_variant	15/15		NP_001121619.1
NF1	NM_000267.3	c.1721+3A>G		splice_region_variant, intron_variant			NP_000258.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NF1	ENST00000358273.9	c.1721+3A>G		splice_region_variant, intron_variant		1	NM_001042492.3	ENSP00000351015.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:15

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Neurofibromatosis, type 1 Pathogenic:8

Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 17, 2024	This sequence change falls in intron 15 of the NF1 gene. It does not directly change the encoded amino acid sequence of the NF1 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individuals with neurofibromatosis type 1 (PMID: 7981679, 15146469, 16944272, 18546366, 23404336, 26478990). This variant is also known as c.1720+3A>G. ClinVar contains an entry for this variant (Variation ID: 374108). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of exon 15 and introduces a premature termination codon (PMID: 7981679; Invitae). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Medical Genetics, University of Parma	Aug 17, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Juno Genomics, Hangzhou Juno Genomics, Inc	-	PM2_Supporting+PS3+PS4_Moderate+PP1+PP4+PM6 -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Apr 08, 2024	Variant summary: NF1 c.1721+3A>G alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Three predict the variant abolishes a 5' splicing donor site. At least two publications report experimental evidence that this variant affects mRNA splicing, resulting in exon skipping leading to a frameshift (Purandare_1994, Pros_2008). The variant was absent in 225584 control chromosomes (gnomAD). c.1721+3A>G has been reported in the literature in multiple individuals affected with Neurofibromatosis Type 1 (e.g. Purandare_1994, De Luca_2004, Griffiths_2006, Pros_2008.) These data indicate that the variant is very likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 7981679, 15146469, 16944272, 18546366). ClinVar contains an entry for this variant (Variation ID: 374108). Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Department of Molecular Diagnostics, Institute of Oncology Ljubljana	Apr 02, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	Nov 16, 2021	PS3, PS4, PP3, PM2 -
Pathogenic, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Mar 15, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Apr 17, 2024	Criteria applied: PVS1,PS2,PS4_MOD,PM2_SUP,PP4 -

not provided Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jun 28, 2023	Non-canonical splice site variant demonstrated to result in skipping of exon 11 (Violante et al., 2013; Esposito et al., 2015); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis is inconclusive as to whether the variant alters gene splicing; Also known as IVS15+3A>G; This variant is associated with the following publications: (PMID: 19845691, 26478990, 7981679, 23404336, 18546366, 26056819, 15146469, 28008555, 10607834, 16944272, 26969325, 10712197, 16380919, 32352596, 31713330, 31370276, 31776437) -
Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Aug 06, 2019	Not found in the total gnomAD dataset, and the data is high quality (0/263140 chr). Variant has been found in 6 or more unrelated symptomatic patients, while absent in large general pop studies. Predicted to negatively affect a known splice site. Damaging to protein function(s) relevant to disease mechanism. Inconclusive segregation with disease. -
Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Jun 22, 2023	PP1, PM2_moderate, PVS1 -

Optic nerve glioma;C1861975:Cafe au lait spots, multiple Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Centre for Mendelian Genomics, University Medical Centre Ljubljana

Jan 01, 2017

- -

Neurofibroma;C1861975:Cafe au lait spots, multiple Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Centre for Mendelian Genomics, University Medical Centre Ljubljana

Dec 01, 2014

- -

Juvenile myelomonocytic leukemia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Jul 12, 2022

- -

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Apr 06, 2015

The c.1721+3A>G intronic pathogenic mutation results from an A to G substitution 3 nucleotides after coding exon 15 in the NF1 gene. This mutation was shown by twoseparate studiestoinduce skipping ofexon11 at the mRNA level, causinga shift in the translational reading frame, leading to premature truncation of the NF1protein(p.Ala548LeufsX13) (PurandareSM, et al. Hum. Mol. Genet. 1994;3(7):1109-15 andPros E, et al. Hum.Mutat. 2008;29(9):E173-93). This mutation has been seen in four individuals who fulfill the NIH diagnostic criteria for NF1 (neurofibromatosis type 1) and in nine individualssuspected of having aNF1 clinical diagnosis. In addition, one of these individuals presented withfeatures of bothNF1 and Noonan syndrome (De Luca A, et al. Am. J. Hum. Genet. 2005;77(6):1092-101,Griffiths S, et al. Fam. Cancer 2007;6(1):21-34,Violante IR, et al. Brain 2013;136(Pt 3):918-25,Purandare SM, et al. Hum. Mol. Genet. 1994;3(7):1109-15,FahsoldR, et al. Am. J. Hum. Genet. 2000;66(3):790-818,andArs E, et al. Hum. Mol. Genet. 2000;9(2):237-47).Based on the available evidence, c.1721+3A>G is classified as a pathogenic mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.14	T
BayesDel_noAF	Benign	-0.43
CADD	Pathogenic	26
DANN	Uncertain	0.99
Eigen	Benign	0.051
Eigen_PC	Uncertain	0.26
FATHMM_MKL	Uncertain	0.84	D
LIST_S2	Benign	0.37	T
M_CAP	Benign	0.021	T
MetaRNN	Benign	0.22	T
MetaSVM	Benign	-0.85	T
PROVEAN	Benign	1.2	N
REVEL	Benign	0.18
Sift	Benign	0.057	T
Sift4G	Benign	0.15	T
Vest4		0.47
MutPred		0.33		Gain of catalytic residue at I573 (P = 0.1473);
MVP		0.64
ClinPred		0.70	D
GERP RS		5.8

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.55		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.55		Position offset: -1
DS_DL_spliceai		0.49		Position offset: -3

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

Publications

LitVar

Other links and lift over

dbSNP: rs1057518904; hg19: chr17-29548950; COSMIC: COSV62193369; COSMIC: COSV62193369;