chr17-31218969-A-ATT
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Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BS2_Supporting
The NM_001042492.3(NF1):c.1528-30_1528-29dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000261 in 1,532,778 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000028 ( 1 hom. )
Consequence
NF1
NM_001042492.3 intron
NM_001042492.3 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.685
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 -1 ACMG points.
BS2
High AC in GnomAdExome4 at 38 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 | UniProt |
---|---|---|---|---|---|---|---|
NF1 | NM_001042492.3 | c.1528-30_1528-29dup | intron_variant | ENST00000358273.9 | |||
NF1 | NM_000267.3 | c.1528-30_1528-29dup | intron_variant | ||||
NF1 | NM_001128147.3 | c.1528-30_1528-29dup | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NF1 | ENST00000358273.9 | c.1528-30_1528-29dup | intron_variant | 1 | NM_001042492.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151736Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.0000275 AC: 38AN: 1381042Hom.: 1 Cov.: 29 AF XY: 0.0000262 AC XY: 18AN XY: 685806
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GnomAD4 genome AF: 0.0000132 AC: 2AN: 151736Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 74080
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at