rs886038397
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_001042492.3(NF1):c.5813-40_5813-39dup variant causes a intron change. The variant allele was found at a frequency of 0.000000765 in 1,306,744 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 30)
Exomes 𝑓: 7.7e-7 ( 0 hom. )
Consequence
NF1
NM_001042492.3 intron
NM_001042492.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.78
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 Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP6
?
Variant 17-31334795-A-ATT is Benign according to our data. Variant chr17-31334795-A-ATT is described in ClinVar as [Likely_benign]. Clinvar id is 257295.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NF1 | NM_001042492.3 | c.5813-40_5813-39dup | intron_variant | ENST00000358273.9 | |||
NF1 | NM_000267.3 | c.5750-40_5750-39dup | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NF1 | ENST00000358273.9 | c.5813-40_5813-39dup | intron_variant | 1 | NM_001042492.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 30
GnomAD3 genomes
?
Cov.:
30
GnomAD4 exome AF: 7.65e-7 AC: 1AN: 1306744Hom.: 0 Cov.: 20 AF XY: 0.00 AC XY: 0AN XY: 658412
GnomAD4 exome
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1
AN:
1306744
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20
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0
AN XY:
658412
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GnomAD4 genome ? Cov.: 30
GnomAD4 genome
?
Cov.:
30
Bravo
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at