chr17-31260526-C-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001042492.3(NF1):c.4577+11C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000974 in 1,613,532 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001042492.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00126 AC: 191AN: 152084Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00112 AC: 280AN: 251056Hom.: 0 AF XY: 0.00105 AC XY: 142AN XY: 135690
GnomAD4 exome AF: 0.000945 AC: 1381AN: 1461330Hom.: 5 Cov.: 31 AF XY: 0.000953 AC XY: 693AN XY: 726974
GnomAD4 genome AF: 0.00125 AC: 191AN: 152202Hom.: 1 Cov.: 32 AF XY: 0.00134 AC XY: 100AN XY: 74400
ClinVar
Submissions by phenotype
not specified Benign:5
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c.4577+11C>G in intron 34 of NF1: This variant is not expected to have clinical significance because it is not located within the conserved splice consensus seq uence. It has been identified in 0.12% (83/66726) of European American chromosom es by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; db SNP rs190614908). -
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Neurofibromatosis, type 1 Benign:4
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not provided Benign:4
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
NF1: BS1, BS2 -
Neurofibromatosis, familial spinal Benign:1
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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. -
Hereditary cancer-predisposing syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at