NM_001303052.2:c.-420-22945G>A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001303052.2(MYT1L):c.-420-22945G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 151,610 control chromosomes in the GnomAD database, including 4,393 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 0.21 ( 4393 hom., cov: 32)
Consequence
MYT1L
NM_001303052.2 intron
NM_001303052.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.679
Publications
7 publications found
Genes affected
MYT1L (HGNC:7623): (myelin transcription factor 1 like) This gene encodes a member of the zinc finger superfamily of transcription factors whose expression, thus far, has been found only in neuronal tissues. The encoded protein belongs to a novel class of cystein-cystein-histidine-cystein zinc finger proteins that function in the developing mammalian central nervous system. Forced expression of this gene in combination with the basic helix-loop-helix transcription factor NeuroD1 and the transcription factors POU class 3 homeobox 2 and achaete-scute family basic helix-loop-helix transcription factor 1 can convert fetal and postnatal human fibroblasts into induced neuronal cells, which are able to generate action potentials. Mutations in this gene have been associated with an autosomal dominant form of cognitive disability and with autism spectrum disorder. Alternative splicing results in multiple variants. [provided by RefSeq, Jul 2017]
MYT1L Gene-Disease associations (from GenCC):
- intellectual disability, autosomal dominant 39Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Genomics England PanelApp, Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
- syndromic intellectual disabilityInheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, ClinGen
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.214 AC: 32350AN: 151492Hom.: 4372 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
32350
AN:
151492
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.214 AC: 32415AN: 151610Hom.: 4393 Cov.: 32 AF XY: 0.209 AC XY: 15497AN XY: 74082 show subpopulations
GnomAD4 genome
AF:
AC:
32415
AN:
151610
Hom.:
Cov.:
32
AF XY:
AC XY:
15497
AN XY:
74082
show subpopulations
African (AFR)
AF:
AC:
16392
AN:
41340
American (AMR)
AF:
AC:
2265
AN:
15218
Ashkenazi Jewish (ASJ)
AF:
AC:
353
AN:
3462
East Asian (EAS)
AF:
AC:
658
AN:
5158
South Asian (SAS)
AF:
AC:
385
AN:
4804
European-Finnish (FIN)
AF:
AC:
1369
AN:
10480
Middle Eastern (MID)
AF:
AC:
37
AN:
294
European-Non Finnish (NFE)
AF:
AC:
10364
AN:
67844
Other (OTH)
AF:
AC:
397
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1192
2384
3576
4768
5960
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
377
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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