chr10-129840997-G-A
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001375380.1(EBF3):c.1408C>T(p.Arg470*) variant causes a stop gained change. The variant allele was found at a frequency of 0.000000684 in 1,461,704 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001375380.1 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EBF3 | NM_001375380.1 | c.1408C>T | p.Arg470* | stop_gained | Exon 14 of 17 | ENST00000440978.2 | NP_001362309.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EBF3 | ENST00000440978.2 | c.1408C>T | p.Arg470* | stop_gained | Exon 14 of 17 | 3 | NM_001375380.1 | ENSP00000387543.2 | ||
EBF3 | ENST00000368648.8 | c.1381C>T | p.Arg461* | stop_gained | Exon 15 of 17 | 1 | ENSP00000357637.3 | |||
EBF3 | ENST00000355311.10 | c.1408C>T | p.Arg470* | stop_gained | Exon 14 of 16 | 5 | ENSP00000347463.4 | |||
EBF3 | ENST00000675373.1 | n.1053C>T | non_coding_transcript_exon_variant | Exon 11 of 14 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251088Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135672
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461704Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727140
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Pathogenic:1
Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Has not been previously published as pathogenic or benign to our knowledge -
Intellectual disability Pathogenic:1
- -
Hypotonia, ataxia, and delayed development syndrome Uncertain:1
_x000D_ Criteria applied: PVS1 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at