chr17-1781332-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_052928.3(SMYD4):c.2369C>A(p.Ser790Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.0000161 in 1,613,806 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_052928.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMYD4 | NM_052928.3 | c.2369C>A | p.Ser790Tyr | missense_variant | Exon 11 of 11 | ENST00000305513.12 | NP_443160.2 | |
SMYD4 | XM_024450560.2 | c.2369C>A | p.Ser790Tyr | missense_variant | Exon 11 of 11 | XP_024306328.1 | ||
SMYD4 | XM_047435291.1 | c.2057C>A | p.Ser686Tyr | missense_variant | Exon 10 of 10 | XP_047291247.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152120Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251458Hom.: 1 AF XY: 0.00 AC XY: 0AN XY: 135910
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461686Hom.: 1 Cov.: 30 AF XY: 0.00000825 AC XY: 6AN XY: 727134
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152120Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74310
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2369C>A (p.S790Y) alteration is located in exon 11 (coding exon 10) of the SMYD4 gene. This alteration results from a C to A substitution at nucleotide position 2369, causing the serine (S) at amino acid position 790 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at