17-1786959-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_052928.3(SMYD4):c.1735C>T(p.Arg579Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000942 in 1,613,820 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R579Q) has been classified as Likely benign.
Frequency
Consequence
NM_052928.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMYD4 | NM_052928.3 | c.1735C>T | p.Arg579Trp | missense_variant | 7/11 | ENST00000305513.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMYD4 | ENST00000305513.12 | c.1735C>T | p.Arg579Trp | missense_variant | 7/11 | 1 | NM_052928.3 | P1 | |
SMYD4 | ENST00000491788.1 | c.1147C>T | p.Arg383Trp | missense_variant | 3/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000916 AC: 23AN: 251056Hom.: 0 AF XY: 0.0000884 AC XY: 12AN XY: 135728
GnomAD4 exome AF: 0.0000965 AC: 141AN: 1461484Hom.: 0 Cov.: 30 AF XY: 0.0000949 AC XY: 69AN XY: 727032
GnomAD4 genome ? AF: 0.0000722 AC: 11AN: 152336Hom.: 0 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74490
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2022 | SMYD4: BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at