chr17-1783378-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_052928.3(SMYD4):c.2119C>T(p.Arg707Trp) variant causes a missense change. The variant allele was found at a frequency of 0.00000682 in 1,612,280 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMYD4 | NM_052928.3 | c.2119C>T | p.Arg707Trp | missense_variant | Exon 9 of 11 | ENST00000305513.12 | NP_443160.2 | |
SMYD4 | XM_024450560.2 | c.2119C>T | p.Arg707Trp | missense_variant | Exon 9 of 11 | XP_024306328.1 | ||
SMYD4 | XM_047435290.1 | c.2119C>T | p.Arg707Trp | missense_variant | Exon 9 of 10 | XP_047291246.1 | ||
SMYD4 | XM_047435291.1 | c.1807C>T | p.Arg603Trp | missense_variant | Exon 8 of 10 | XP_047291247.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMYD4 | ENST00000305513.12 | c.2119C>T | p.Arg707Trp | missense_variant | Exon 9 of 11 | 1 | NM_052928.3 | ENSP00000304360.7 | ||
SMYD4 | ENST00000491788.1 | c.1531C>T | p.Arg511Trp | missense_variant | Exon 5 of 6 | 2 | ENSP00000460921.1 | |||
SMYD4 | ENST00000476292.1 | n.486C>T | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000799 AC: 2AN: 250464Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135604
GnomAD4 exome AF: 0.00000685 AC: 10AN: 1460070Hom.: 0 Cov.: 32 AF XY: 0.00000551 AC XY: 4AN XY: 726346
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2119C>T (p.R707W) alteration is located in exon 9 (coding exon 8) of the SMYD4 gene. This alteration results from a C to T substitution at nucleotide position 2119, causing the arginine (R) at amino acid position 707 to be replaced by a tryptophan (W). 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