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rs10082479

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020549.5(CHAT):c.698+560A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,190 control chromosomes in the GnomAD database, including 5,215 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.23 ( 5215 hom., cov: 33)

Consequence

CHAT
NM_020549.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.305
Variant links:
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CHATNM_020549.5 linkuse as main transcriptc.698+560A>T intron_variant ENST00000337653.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CHATENST00000337653.7 linkuse as main transcriptc.698+560A>T intron_variant 1 NM_020549.5 P2P28329-1

Frequencies

GnomAD3 genomes
AF:
0.225
AC:
34177
AN:
152072
Hom.:
5173
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.410
Gnomad AMI
AF:
0.143
Gnomad AMR
AF:
0.323
Gnomad ASJ
AF:
0.162
Gnomad EAS
AF:
0.232
Gnomad SAS
AF:
0.117
Gnomad FIN
AF:
0.136
Gnomad MID
AF:
0.130
Gnomad NFE
AF:
0.117
Gnomad OTH
AF:
0.192
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.225
AC:
34286
AN:
152190
Hom.:
5215
Cov.:
33
AF XY:
0.227
AC XY:
16885
AN XY:
74400
show subpopulations
Gnomad4 AFR
AF:
0.411
Gnomad4 AMR
AF:
0.324
Gnomad4 ASJ
AF:
0.162
Gnomad4 EAS
AF:
0.233
Gnomad4 SAS
AF:
0.117
Gnomad4 FIN
AF:
0.136
Gnomad4 NFE
AF:
0.117
Gnomad4 OTH
AF:
0.199
Alfa
AF:
0.183
Hom.:
440
Bravo
AF:
0.255

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
Cadd
Benign
1.8
Dann
Benign
0.83

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10082479; hg19: chr10-50829219; API