chr1-154571682-G-C
Variant summary
Our verdict is Pathogenic. Variant got 15 ACMG points: 15P and 0B. PS1_Very_StrongPM2PM5PP3_ModeratePP5
The NM_000748.3(CHRNB2):c.859G>C(p.Val287Leu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V287M) has been classified as Pathogenic.
Frequency
Consequence
NM_000748.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNB2 | NM_000748.3 | c.859G>C | p.Val287Leu | missense_variant | 5/6 | ENST00000368476.4 | |
CHRNB2 | XM_017000180.3 | c.349G>C | p.Val117Leu | missense_variant | 2/3 | ||
CHRNB2 | XR_001736952.3 | n.1126G>C | non_coding_transcript_exon_variant | 5/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNB2 | ENST00000368476.4 | c.859G>C | p.Val287Leu | missense_variant | 5/6 | 1 | NM_000748.3 | P4 | |
CHRNB2 | ENST00000637900.1 | c.865G>C | p.Val289Leu | missense_variant | 5/6 | 5 | A1 | ||
CHRNB2 | ENST00000636034.1 | c.859G>C | p.Val287Leu | missense_variant, NMD_transcript_variant | 5/9 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 33
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Autosomal dominant nocturnal frontal lobe epilepsy 3 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 01, 2000 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at