rs11101192
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_020549.5(CHAT):c.1281+47G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0174 in 1,600,960 control chromosomes in the GnomAD database, including 2,189 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.029 ( 276 hom., cov: 33)
Exomes 𝑓: 0.016 ( 1913 hom. )
Consequence
CHAT
NM_020549.5 intron
NM_020549.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.24
Genes affected
CHAT (HGNC:1912): (choline O-acetyltransferase) This gene encodes an enzyme which catalyzes the biosynthesis of the neurotransmitter acetylcholine. This gene product is a characteristic feature of cholinergic neurons, and changes in these neurons may explain some of the symptoms of Alzheimer's disease. Polymorphisms in this gene have been associated with Alzheimer's disease and mild cognitive impairment. Mutations in this gene are associated with congenital myasthenic syndrome associated with episodic apnea. Multiple transcript variants encoding different isoforms have been found for this gene, and some of these variants have been shown to encode more than one isoform. [provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 10-49646721-G-A is Benign according to our data. Variant chr10-49646721-G-A is described in ClinVar as [Benign]. Clinvar id is 261329.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHAT | NM_020549.5 | c.1281+47G>A | intron_variant | ENST00000337653.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHAT | ENST00000337653.7 | c.1281+47G>A | intron_variant | 1 | NM_020549.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0286 AC: 4357AN: 152202Hom.: 276 Cov.: 33
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GnomAD3 exomes AF: 0.0550 AC: 12795AN: 232518Hom.: 1222 AF XY: 0.0481 AC XY: 6077AN XY: 126226
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GnomAD4 exome AF: 0.0162 AC: 23482AN: 1448642Hom.: 1913 Cov.: 30 AF XY: 0.0161 AC XY: 11565AN XY: 720548
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GnomAD4 genome ? AF: 0.0287 AC: 4364AN: 152318Hom.: 276 Cov.: 33 AF XY: 0.0306 AC XY: 2276AN XY: 74480
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 08, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at