10-49627760-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_020549.5(CHAT):c.1086C>T(p.Ala362=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000147 in 1,613,796 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A362A) has been classified as Likely benign.
Frequency
Consequence
NM_020549.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHAT | NM_020549.5 | c.1086C>T | p.Ala362= | synonymous_variant | 7/15 | ENST00000337653.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHAT | ENST00000337653.7 | c.1086C>T | p.Ala362= | synonymous_variant | 7/15 | 1 | NM_020549.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000854 AC: 13AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000558 AC: 14AN: 251072Hom.: 0 AF XY: 0.0000737 AC XY: 10AN XY: 135714
GnomAD4 exome AF: 0.000154 AC: 225AN: 1461606Hom.: 0 Cov.: 32 AF XY: 0.000158 AC XY: 115AN XY: 727114
GnomAD4 genome ? AF: 0.0000854 AC: 13AN: 152190Hom.: 0 Cov.: 33 AF XY: 0.0000942 AC XY: 7AN XY: 74340
ClinVar
Submissions by phenotype
Familial infantile myasthenia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at