17-31232069-T-TTTC
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP6_ModerateBS2_Supporting
The ENST00000358273.9(NF1):c.3198-4_3198-3insTTC variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000048 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000034 ( 0 hom. )
Consequence
NF1
ENST00000358273.9 splice_region, splice_polypyrimidine_tract, intron
ENST00000358273.9 splice_region, splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.140
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
BP6
Variant 17-31232069-T-TTTC is Benign according to our data. Variant chr17-31232069-T-TTTC is described in ClinVar as [Likely_benign]. Clinvar id is 457631.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 7 AD gene. Variant has AC lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NF1 | NM_001042492.3 | c.3198-4_3198-3insTTC | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000358273.9 | NP_001035957.1 | |||
NF1 | NM_000267.3 | c.3198-4_3198-3insTTC | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NP_000258.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NF1 | ENST00000358273.9 | c.3198-4_3198-3insTTC | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001042492.3 | ENSP00000351015 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000479 AC: 7AN: 145986Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.00000344 AC: 4AN: 1161256Hom.: 0 Cov.: 3 AF XY: 0.00000172 AC XY: 1AN XY: 581726
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GnomAD4 genome AF: 0.0000479 AC: 7AN: 145986Hom.: 0 Cov.: 0 AF XY: 0.0000702 AC XY: 5AN XY: 71198
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Neurofibromatosis, type 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 18, 2024 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at