rs144323841
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_024757.5(EHMT1):c.390G>A(p.Pro130=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000893 in 1,612,916 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. P130P) 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 -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EHMT1 | NM_024757.5 | c.390G>A | p.Pro130= | synonymous_variant | 3/27 | ENST00000460843.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EHMT1 | ENST00000460843.6 | c.390G>A | p.Pro130= | synonymous_variant | 3/27 | 5 | NM_024757.5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152134Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000188 AC: 47AN: 250588Hom.: 0 AF XY: 0.000228 AC XY: 31AN XY: 135702
GnomAD4 exome AF: 0.0000904 AC: 132AN: 1460664Hom.: 2 Cov.: 31 AF XY: 0.000133 AC XY: 97AN XY: 726626
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152252Hom.: 0 Cov.: 31 AF XY: 0.000121 AC XY: 9AN XY: 74420
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 07, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2023 | EHMT1: BP4, BP7, BS1 - |
Kleefstra syndrome 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 08, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at