rs112664025
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_024757.5(EHMT1):c.3375-11_3375-10del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0589 in 1,613,552 control chromosomes in the GnomAD database, including 3,276 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.052 ( 241 hom., cov: 32)
Exomes 𝑓: 0.060 ( 3035 hom. )
Consequence
EHMT1
NM_024757.5 splice_polypyrimidine_tract, intron
NM_024757.5 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.0480
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 made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
?
Variant 9-137817423-ACT-A is Benign according to our data. Variant chr9-137817423-ACT-A is described in ClinVar as [Benign]. Clinvar id is 96154.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-137817423-ACT-A is described in Lovd as [Likely_benign].
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EHMT1 | NM_024757.5 | c.3375-11_3375-10del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000460843.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EHMT1 | ENST00000460843.6 | c.3375-11_3375-10del | splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_024757.5 |
Frequencies
GnomAD3 genomes ? AF: 0.0515 AC: 7821AN: 151730Hom.: 236 Cov.: 32
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GnomAD3 exomes AF: 0.0549 AC: 13758AN: 250808Hom.: 530 AF XY: 0.0594 AC XY: 8064AN XY: 135654
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GnomAD4 exome AF: 0.0596 AC: 87168AN: 1461704Hom.: 3035 AF XY: 0.0617 AC XY: 44884AN XY: 727178
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GnomAD4 genome ? AF: 0.0516 AC: 7840AN: 151848Hom.: 241 Cov.: 32 AF XY: 0.0514 AC XY: 3813AN XY: 74194
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 26, 2013 | - - |
Kleefstra syndrome 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 09, 2019 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at