17-1784413-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_052928.3(SMYD4):c.1933G>A(p.Val645Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00321 in 1,614,208 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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 -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMYD4 | NM_052928.3 | c.1933G>A | p.Val645Ile | missense_variant | 8/11 | ENST00000305513.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMYD4 | ENST00000305513.12 | c.1933G>A | p.Val645Ile | missense_variant | 8/11 | 1 | NM_052928.3 | P1 | |
SMYD4 | ENST00000491788.1 | c.1345G>A | p.Val449Ile | missense_variant | 4/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00251 AC: 382AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00206 AC: 517AN: 251486Hom.: 1 AF XY: 0.00199 AC XY: 270AN XY: 135920
GnomAD4 exome AF: 0.00329 AC: 4803AN: 1461876Hom.: 11 Cov.: 30 AF XY: 0.00312 AC XY: 2270AN XY: 727238
GnomAD4 genome ? AF: 0.00251 AC: 382AN: 152332Hom.: 0 Cov.: 33 AF XY: 0.00235 AC XY: 175AN XY: 74480
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