chr2-174753570-G-C
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PS1PM1PM2PP3PP5
The NM_000079.4(CHRNA1):c.711C>G(p.Asn237Lys) variant causes a missense change involving the alteration of a non-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 nucleotide change resulting in same amino acid change has been previously reported as Pathogenicin ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N237I) has been classified as Uncertain significance.
Frequency
Consequence
NM_000079.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNA1 | NM_000079.4 | c.711C>G | p.Asn237Lys | missense_variant | 6/9 | ENST00000348749.9 | |
CHRNA1 | NM_001039523.3 | c.786C>G | p.Asn262Lys | missense_variant | 7/10 | ||
CHRNA1 | XM_017003256.2 | c.807C>G | p.Asn269Lys | missense_variant | 6/9 | ||
CHRNA1 | XM_017003257.2 | c.732C>G | p.Asn244Lys | missense_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNA1 | ENST00000348749.9 | c.711C>G | p.Asn237Lys | missense_variant | 6/9 | 1 | NM_000079.4 | P1 | |
ENST00000442996.1 | n.322-19179G>C | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
Congenital myasthenic syndrome 1A Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 01, 1996 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at