rs376810828
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_ModerateBP7BS1BS2_Supporting
The NM_024757.5(EHMT1):c.276G>A(p.Ala92=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000601 in 1,613,302 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. A92A) has been classified as Likely benign.
Frequency
Consequence
NM_024757.5 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EHMT1 | NM_024757.5 | c.276G>A | p.Ala92= | synonymous_variant | 3/27 | ENST00000460843.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EHMT1 | ENST00000460843.6 | c.276G>A | p.Ala92= | synonymous_variant | 3/27 | 5 | NM_024757.5 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152110Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000996 AC: 25AN: 250886Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135788
GnomAD4 exome AF: 0.0000623 AC: 91AN: 1461076Hom.: 0 Cov.: 31 AF XY: 0.0000757 AC XY: 55AN XY: 726808
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74416
ClinVar
Submissions by phenotype
Kleefstra syndrome 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at