chr2-174754305-C-G
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_000079.4(CHRNA1):c.454G>C(p.Val152Leu) variant causes a missense change involving the alteration of a conserved nucleotide. 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. V152I) has been classified as Uncertain significance.
Frequency
Consequence
NM_000079.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNA1 | NM_000079.4 | c.454G>C | p.Val152Leu | missense_variant | 5/9 | ENST00000348749.9 | |
CHRNA1 | NM_001039523.3 | c.529G>C | p.Val177Leu | missense_variant | 6/10 | ||
CHRNA1 | XM_017003256.2 | c.550G>C | p.Val184Leu | missense_variant | 5/9 | ||
CHRNA1 | XM_017003257.2 | c.475G>C | p.Val159Leu | missense_variant | 4/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNA1 | ENST00000348749.9 | c.454G>C | p.Val152Leu | missense_variant | 5/9 | 1 | NM_000079.4 | P1 | |
ENST00000442996.1 | n.322-18444C>G | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Myasthenic syndrome, congenital, 1B, fast-channel Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 01, 2003 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at