chr10-20819519-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000377122.9(NEBL):c.1963-3C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,660 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000377122.9 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NEBL | NM_006393.3 | c.1963-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000377122.9 | NP_006384.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEBL | ENST00000377122.9 | c.1963-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_006393.3 | ENSP00000366326 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461660Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 727142
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jul 17, 2014 | The 1963-3C>T variant in NEBL has not been reported in individuals with cardiomy opathy or in large population studies. This variant is located in the 3' splice region. Computational tools do not suggest an impact to splicing; however, this information is not predictive enough to rule out pathogenicity. In addition, all published variants in NEBL are missense variants and the significance of varian ts that may cause loss of protein function remains unclear. In summary, the clin ical significance of the 1963-3C>T variant is uncertain. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at