rs115212829
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP3BP4_StrongBP6_Very_StrongBS1BS2
The NM_020549.5(CHAT):āc.1135G>Cā(p.Asp379His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000518 in 1,614,242 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. D379D) has been classified as Likely benign.
Frequency
Consequence
NM_020549.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHAT | NM_020549.5 | c.1135G>C | p.Asp379His | missense_variant | 8/15 | ENST00000337653.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHAT | ENST00000337653.7 | c.1135G>C | p.Asp379His | missense_variant | 8/15 | 1 | NM_020549.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00278 AC: 423AN: 152252Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.000621 AC: 156AN: 251370Hom.: 1 AF XY: 0.000456 AC XY: 62AN XY: 135894
GnomAD4 exome AF: 0.000283 AC: 413AN: 1461872Hom.: 2 Cov.: 32 AF XY: 0.000246 AC XY: 179AN XY: 727240
GnomAD4 genome ? AF: 0.00278 AC: 423AN: 152370Hom.: 3 Cov.: 33 AF XY: 0.00263 AC XY: 196AN XY: 74504
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 29, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Familial infantile myasthenia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 07, 2021 | This variant is associated with the following publications: (PMID: 26582918) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at