rs1554896995
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_024757.5(EHMT1):c.3183C>T(p.Tyr1061=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000822 in 1,459,332 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_024757.5 splice_region, synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EHMT1 | NM_024757.5 | c.3183C>T | p.Tyr1061= | splice_region_variant, synonymous_variant | 22/27 | ENST00000460843.6 | NP_079033.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EHMT1 | ENST00000460843.6 | c.3183C>T | p.Tyr1061= | splice_region_variant, synonymous_variant | 22/27 | 5 | NM_024757.5 | ENSP00000417980 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000822 AC: 12AN: 1459332Hom.: 0 Cov.: 31 AF XY: 0.00000826 AC XY: 6AN XY: 726102
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Kleefstra syndrome 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 27, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at