9-137619034-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_024757.5(EHMT1):c.6C>T(p.Ala2Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000122 in 821,020 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000012 ( 0 hom. )
Consequence
EHMT1
NM_024757.5 synonymous
NM_024757.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.67
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]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP6
Variant 9-137619034-C-T is Benign according to our data. Variant chr9-137619034-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2875184.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=2.67 with no splicing effect.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD4 exome AF: 0.00000122 AC: 1AN: 821020Hom.: 0 Cov.: 16 AF XY: 0.00000263 AC XY: 1AN XY: 379710 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
821020
Hom.:
Cov.:
16
AF XY:
AC XY:
1
AN XY:
379710
show subpopulations
African (AFR)
AF:
AC:
0
AN:
15520
American (AMR)
AF:
AC:
0
AN:
1078
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
5162
East Asian (EAS)
AF:
AC:
0
AN:
3648
South Asian (SAS)
AF:
AC:
0
AN:
16984
European-Finnish (FIN)
AF:
AC:
0
AN:
528
Middle Eastern (MID)
AF:
AC:
0
AN:
1604
European-Non Finnish (NFE)
AF:
AC:
1
AN:
749578
Other (OTH)
AF:
AC:
0
AN:
26918
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
31
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Kleefstra syndrome 1 Benign:1
Mar 20, 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
RBP_binding_hub_radar
RBP_regulation_power_radar
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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