rs139461232
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_024757.5(EHMT1):c.432C>G(p.Ala144=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,611,028 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 (★). Synonymous variant affecting the same amino acid position (i.e. A144A) has been classified as Likely benign.
Frequency
Consequence
NM_024757.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EHMT1 | NM_024757.5 | c.432C>G | p.Ala144= | synonymous_variant | 3/27 | ENST00000460843.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EHMT1 | ENST00000460843.6 | c.432C>G | p.Ala144= | synonymous_variant | 3/27 | 5 | NM_024757.5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000986 AC: 15AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250344Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135552
GnomAD4 exome AF: 0.00000960 AC: 14AN: 1458876Hom.: 0 Cov.: 31 AF XY: 0.00000551 AC XY: 4AN XY: 725310
GnomAD4 genome ? AF: 0.0000986 AC: 15AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74314
ClinVar
Submissions by phenotype
Kleefstra syndrome 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 28, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at