rs652888
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006709.5(EHMT2):c.2917-18T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 1,607,448 control chromosomes in the GnomAD database, including 38,123 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 0.20 ( 3249 hom., cov: 32)
Exomes 𝑓: 0.21 ( 34874 hom. )
Consequence
EHMT2
NM_006709.5 intron
NM_006709.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.470
Genes affected
EHMT2 (HGNC:14129): (euchromatic histone lysine methyltransferase 2) This gene encodes a methyltransferase that methylates lysine residues of histone H3. Methylation of H3 at lysine 9 by this protein results in recruitment of additional epigenetic regulators and repression of transcription. This gene was initially thought to be two different genes, NG36 and G9a, adjacent to each other in the HLA locus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
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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=-0.87).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EHMT2 | NM_006709.5 | c.2917-18T>C | intron_variant | ENST00000375537.9 | |||
EHMT2-AS1 | NR_174947.1 | n.1824A>G | non_coding_transcript_exon_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EHMT2 | ENST00000375537.9 | c.2917-18T>C | intron_variant | 1 | NM_006709.5 | ||||
EHMT2-AS1 | ENST00000642849.1 | n.1824A>G | non_coding_transcript_exon_variant | 5/5 |
Frequencies
GnomAD3 genomes ? AF: 0.202 AC: 30699AN: 152014Hom.: 3253 Cov.: 32
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GnomAD3 exomes AF: 0.183 AC: 42817AN: 234268Hom.: 4232 AF XY: 0.184 AC XY: 23581AN XY: 127876
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GnomAD4 exome AF: 0.213 AC: 309556AN: 1455316Hom.: 34874 Cov.: 34 AF XY: 0.210 AC XY: 152027AN XY: 723556
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GnomAD4 genome ? AF: 0.202 AC: 30703AN: 152132Hom.: 3249 Cov.: 32 AF XY: 0.199 AC XY: 14814AN XY: 74368
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at