rs199780189
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM1BP6BS2_Supporting
The NM_024757.5(EHMT1):c.3322G>A(p.Ala1108Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000372 in 1,613,120 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. A1108A) has been classified as Likely benign.
Frequency
Consequence
NM_024757.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EHMT1 | NM_024757.5 | c.3322G>A | p.Ala1108Thr | missense_variant | 23/27 | ENST00000460843.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EHMT1 | ENST00000460843.6 | c.3322G>A | p.Ala1108Thr | missense_variant | 23/27 | 5 | NM_024757.5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152178Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000281 AC: 7AN: 249378Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134802
GnomAD4 exome AF: 0.0000377 AC: 55AN: 1460824Hom.: 0 Cov.: 30 AF XY: 0.0000399 AC XY: 29AN XY: 726586
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152296Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74480
ClinVar
Submissions by phenotype
Kleefstra syndrome 1 Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Oct 06, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at