17-31228914-TTTACATTTTTTGTACTTTTGTCATGGAAGAAATGTTGGATAAAGCATAATTTGTCAAGTCTCAACTAATTAAGGTTTAATTCATGCTTTGCACAAAAATTTTGTGTTTAGGCTGCTGAAAGCCTTCACAAGACCATTGTTAAGAGGCGAATGTCCCATGTGAGTGGAGGAGGATCCATAGATTTGTCTGACACAGACTCCCTACAGGAATGGATCAACATGACTGGCTTCCTTTGTGCCCTTGGGGGAGTGTGCCTCCAGCAGAGAAGCAATTCTGGCCTGGCAACCTATAGCCCACCCATGGGTCCAGTCAGTGAACGTAAGGGTTCTATGATTTCAGTGATGTCTTCAGAGGGAAACGCAGATACACCTGTCAGCAAATTTATGGATCGGCTGTTGTCCTTAATGGTGTGTAACCATGAGAAAGTGGGACTTCAAATACGGACCAATGTTAAGGATCTGGTGGGTCTAGAATTGAGTCCTGCTCTGTATCCAATGCTATTTAACAAATTGAAGAATACCATCAGCAAGTTTTTTGACTCCCAAGGACAGGTAAAGTGTTCTCTTATTTTTCACCTTTCTCTATGAATAGAGTGACTTGTTTGAAATAAGCCTTT-TAAAA

Position:

• chr17-31228914-TTTACATTTTTTGTACTTTTGTCATGGAAGAAATGTTGGATAAAGCATAATTTGTCAAGTCTCAACTAATTAAGGTTTAATTCATGCTTTGCACAAAAATTTTGTGTTTAGGCTGCTGAAAGCCTTCACAAGACCATTGTTAAGAGGCGAATGTCCCATGTGAGTGGAGGAGGATCCATAGATTTGTCTGACACAGACTCCCTACAGGAATGGATCAACATGACTGGCTTCCTTTGTGCCCTTGGGGGAGTGTGCCTCCAGCAGAGAAGCAATTCTGGCCTGGCAACCTATAGCCCACCCATGGGTCCAGTCAGTGAACGTAAGGGTTCTATGATTTCAGTGATGTCTTCAGAGGGAAACGCAGATACACCTGTCAGCAAATTTATGGATCGGCTGTTGTCCTTAATGGTGTGTAACCATGAGAAAGTGGGACTTCAAATACGGACCAATGTTAAGGATCTGGTGGGTCTAGAATTGAGTCCTGCTCTGTATCCAATGCTATTTAACAAATTGAAGAATACCATCAGCAAGTTTTTTGACTCCCAAGGACAGGTAAAGTGTTCTCTTATTTTTCACCTTTCTCTATGAATAGAGTGACTTGTTTGAAATAAGCCTTT-TAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PVS1_Moderate PM2 PP5

The NM_001042492.3(NF1):​c.2410-110_2850+65delinsAAAA variant causes a splice acceptor, splice donor, splice donor 5th base, coding sequence, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: NF1 NM_001042492.3 splice_acceptor, splice_donor, splice_donor_5th_base, coding_sequence, intron
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 1.16

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 Uncertain_significance. Variant got 5 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.051643193 fraction of the gene. No cryptic splice site detected. Exon removal is inframe change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 17-31228915-TTACATTTTTTGTACTTTTGTCATGGAAGAAATGTTGGATAAAGCATAATTTGTCAAGTCTCAACTAATTAAGGTTTAATTCATGCTTTGCACAAAAATTTTGTGTTTAGGCTGCTGAAAGCCTTCACAAGACCATTGTTAAGAGGCGAATGTCCCATGTGAGTGGAGGAGGATCCATAGATTTGTCTGACACAGACTCCCTACAGGAATGGATCAACATGACTGGCTTCCTTTGTGCCCTTGGGGGAGTGTGCCTCCAGCAGAGAAGCAATTCTGGCCTGGCAACCTATAGCCCACCCATGGGTCCAGTCAGTGAACGTAAGGGTTCTATGATTTCAGTGATGTCTTCAGAGGGAAACGCAGATACACCTGTCAGCAAATTTATGGATCGGCTGTTGTCCTTAATGGTGTGTAACCATGAGAAAGTGGGACTTCAAATACGGACCAATGTTAAGGATCTGGTGGGTCTAGAATTGAGTCCTGCTCTGTATCCAATGCTATTTAACAAATTGAAGAATACCATCAGCAAGTTTTTTGACTCCCAAGGACAGGTAAAGTGTTCTCTTATTTTTCACCTTTCTCTATGAATAGAGTGACTTGTTTGAAATAAGCCTTT-AAAA is Pathogenic according to our data. Variant chr17-31228915-TTACATTTTTTGTACTTTTGTCATGGAAGAAATGTTGGATAAAGCATAATTTGTCAAGTCTCAACTAATTAAGGTTTAATTCATGCTTTGCACAAAAATTTTGTGTTTAGGCTGCTGAAAGCCTTCACAAGACCATTGTTAAGAGGCGAATGTCCCATGTGAGTGGAGGAGGATCCATAGATTTGTCTGACACAGACTCCCTACAGGAATGGATCAACATGACTGGCTTCCTTTGTGCCCTTGGGGGAGTGTGCCTCCAGCAGAGAAGCAATTCTGGCCTGGCAACCTATAGCCCACCCATGGGTCCAGTCAGTGAACGTAAGGGTTCTATGATTTCAGTGATGTCTTCAGAGGGAAACGCAGATACACCTGTCAGCAAATTTATGGATCGGCTGTTGTCCTTAATGGTGTGTAACCATGAGAAAGTGGGACTTCAAATACGGACCAATGTTAAGGATCTGGTGGGTCTAGAATTGAGTCCTGCTCTGTATCCAATGCTATTTAACAAATTGAAGAATACCATCAGCAAGTTTTTTGACTCCCAAGGACAGGTAAAGTGTTCTCTTATTTTTCACCTTTCTCTATGAATAGAGTGACTTGTTTGAAATAAGCCTTT-AAAA is described in ClinVar as [Pathogenic]. Clinvar id is 217073.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NF1	NM_001042492.3	c.2410-110_2850+65delinsAAAA		splice_acceptor_variant, splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant	21/58	ENST00000358273.9
NF1	NM_000267.3	c.2410-110_2850+65delinsAAAA		splice_acceptor_variant, splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant	21/57

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NF1	ENST00000358273.9	c.2410-110_2850+65delinsAAAA		splice_acceptor_variant, splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant	21/58	1	NM_001042492.3	P1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Neurofibromatosis, type 1 Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

UAB Medical Genomics Laboratory, UAB Medicine

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1555614169; hg19: chr17-29555933;