17-1786877-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_052928.3(SMYD4):c.1817C>T(p.Ala606Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,614,212 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251466Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135914
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461880Hom.: 0 Cov.: 30 AF XY: 0.0000399 AC XY: 29AN XY: 727244
GnomAD4 genome AF: 0.00000656 AC: 1AN: 152332Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74494
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1817C>T (p.A606V) 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 1817, causing the alanine (A) at amino acid position 606 to be replaced by a valine (V). 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