NM_024757.5:c.3864C>T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_024757.5(EHMT1):c.3864C>T(p.Asp1288Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
EHMT1
NM_024757.5 synonymous
NM_024757.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.74
Publications
0 publications found
Genes affected
EHMT1 (HGNC:24650): (euchromatic histone lysine methyltransferase 1) The protein encoded by this gene is a histone methyltransferase that methylates the lysine-9 position of histone H3. This action marks the genomic region packaged with these methylated histones for transcriptional repression. This protein may be involved in the silencing of MYC- and E2F-responsive genes and therefore could play a role in the G0/G1 cell cycle transition. Defects in this gene are a cause of chromosome 9q subtelomeric deletion syndrome (9q-syndrome, also known as Kleefstra syndrome). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2017]
EHMT1 Gene-Disease associations (from GenCC):
- Kleefstra syndromeInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- Kleefstra syndrome 1Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
Variant 9-137834920-C-T is Benign according to our data. Variant chr9-137834920-C-T is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 210927.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1418638Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 703316
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1418638
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
703316
African (AFR)
AF:
AC:
0
AN:
32180
American (AMR)
AF:
AC:
0
AN:
38058
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24804
East Asian (EAS)
AF:
AC:
0
AN:
38044
South Asian (SAS)
AF:
AC:
0
AN:
82526
European-Finnish (FIN)
AF:
AC:
0
AN:
46818
Middle Eastern (MID)
AF:
AC:
0
AN:
4220
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1093492
Other (OTH)
AF:
AC:
0
AN:
58496
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not specified Uncertain:1
May 06, 2015
Genetic Services Laboratory, University of Chicago
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Kleefstra syndrome 1 Benign:1
Aug 24, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational 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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