17-31232069-T-TTC
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6_Very_StrongBS2_Supporting
The NM_001042492.3(NF1):c.3198-4_3198-3insTC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001042492.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NF1 | NM_001042492.3 | c.3198-4_3198-3insTC | splice_region_variant, intron_variant | Intron 24 of 57 | ENST00000358273.9 | NP_001035957.1 | ||
NF1 | NM_000267.3 | c.3198-4_3198-3insTC | splice_region_variant, intron_variant | Intron 24 of 56 | NP_000258.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000103 AC: 15AN: 145988Hom.: 0 Cov.: 0
GnomAD4 exome AF: 0.0000146 AC: 17AN: 1161250Hom.: 0 Cov.: 3 AF XY: 0.0000120 AC XY: 7AN XY: 581722
GnomAD4 genome AF: 0.000116 AC: 17AN: 146058Hom.: 1 Cov.: 0 AF XY: 0.0000982 AC XY: 7AN XY: 71290
ClinVar
Submissions by phenotype
Neurofibromatosis, type 1 Benign:1
- -
Hereditary cancer-predisposing syndrome;CN230736:Cardiovascular phenotype Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at