17-1786959-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
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 Conflicting classifications of pathogenicity (no stars). 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 -1 ACMG points.
Transcripts
RefSeq
Ensembl
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 specified Uncertain:1
The c.1735C>T (p.R579W) alteration is located in exon 7 (coding exon 6) of the SMYD4 gene. This alteration results from a C to T substitution at nucleotide position 1735, causing the arginine (R) at amino acid position 579 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Benign:1
SMYD4: BP4 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at