13-59666667-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_ModerateBS2
The NM_001042517.2(DIAPH3):c.3499G>A(p.Glu1167Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00000342 in 1,461,664 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_001042517.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DIAPH3 | ENST00000400324.9 | c.3499G>A | p.Glu1167Lys | missense_variant | Exon 28 of 28 | 1 | NM_001042517.2 | ENSP00000383178.3 | ||
DIAPH3 | ENST00000400319.5 | c.3289G>A | p.Glu1097Lys | missense_variant | Exon 26 of 26 | 1 | ENSP00000383173.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249532Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135382
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461664Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 727122
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
DIAPH3-related disorder Uncertain:1
The DIAPH3 c.3499G>A variant is predicted to result in the amino acid substitution p.Glu1167Lys. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.00088% of alleles in individuals of European (Non-Finnish) descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at