rs1555619423
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1PM2PM5PP2
The NM_001042492.3(NF1):c.4835G>A(p.Arg1612Lys) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1612G) has been classified as Pathogenic.
Frequency
Consequence
NM_001042492.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NF1 | NM_001042492.3 | c.4835G>A | p.Arg1612Lys | missense_variant, splice_region_variant | 36/58 | ENST00000358273.9 | NP_001035957.1 | |
NF1 | NM_000267.3 | c.4772G>A | p.Arg1591Lys | missense_variant, splice_region_variant | 35/57 | NP_000258.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NF1 | ENST00000358273.9 | c.4835G>A | p.Arg1612Lys | missense_variant, splice_region_variant | 36/58 | 1 | NM_001042492.3 | ENSP00000351015.4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 26
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
NF1-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 20, 2023 | The NF1 c.4835G>A variant is predicted to result in the amino acid substitution p.Arg1612Lys. This variant occurs at the last nucleotide of the exon and is predicted to slightly weaken the canonical splice donor site (Alamut Visual Plus 1.6.1). To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Hereditary cancer-predisposing syndrome;CN230736:Cardiovascular phenotype Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 06, 2017 | The c.4772G>A variant (also known as p.R1591K), located in coding exon 35 of the NF1 gene, results from a G to A substitution at nucleotide position 4772. The amino acid change results in arginine to lysine at codon 1591, an amino acid with highly similar properties. However, this change occurs in the last base pair of coding exon 35, which makes it likely to have some effect on normal mRNA splicing. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at