17-1781371-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_052928.3(SMYD4):āc.2330C>Gā(p.Pro777Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000651 in 1,613,978 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
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.2330C>G | p.Pro777Arg | missense_variant | Exon 11 of 11 | ENST00000305513.12 | NP_443160.2 | |
SMYD4 | XM_024450560.2 | c.2330C>G | p.Pro777Arg | missense_variant | Exon 11 of 11 | XP_024306328.1 | ||
SMYD4 | XM_047435291.1 | c.2018C>G | p.Pro673Arg | missense_variant | Exon 10 of 10 | XP_047291247.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152132Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251458Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135910
GnomAD4 exome AF: 0.0000664 AC: 97AN: 1461846Hom.: 0 Cov.: 30 AF XY: 0.0000536 AC XY: 39AN XY: 727228
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152132Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2330C>G (p.P777R) alteration is located in exon 11 (coding exon 10) of the SMYD4 gene. This alteration results from a C to G substitution at nucleotide position 2330, causing the proline (P) at amino acid position 777 to be replaced by an arginine (R). 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