rs202208554
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_024757.5(EHMT1):c.102C>G(p.Ala34=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000598 in 1,572,952 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. A34A) 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 -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EHMT1 | NM_024757.5 | c.102C>G | p.Ala34= | synonymous_variant | 3/27 | ENST00000460843.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EHMT1 | ENST00000460843.6 | c.102C>G | p.Ala34= | synonymous_variant | 3/27 | 5 | NM_024757.5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000461 AC: 7AN: 151862Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000179 AC: 4AN: 223596Hom.: 0 AF XY: 0.00000831 AC XY: 1AN XY: 120382
GnomAD4 exome AF: 0.0000612 AC: 87AN: 1421090Hom.: 0 Cov.: 31 AF XY: 0.0000755 AC XY: 53AN XY: 701990
GnomAD4 genome ? AF: 0.0000461 AC: 7AN: 151862Hom.: 0 Cov.: 31 AF XY: 0.0000809 AC XY: 6AN XY: 74136
ClinVar
Submissions by phenotype
Kleefstra syndrome 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 20, 2023 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 24, 2020 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
EHMT1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 15, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at