X-96758210-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6BP7BS2
The NM_006729.5(DIAPH2):c.399C>T(p.Thr133Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000291 in 1,203,448 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_006729.5 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DIAPH2 | ENST00000324765.13 | c.399C>T | p.Thr133Thr | synonymous_variant | Exon 4 of 27 | 1 | NM_006729.5 | ENSP00000321348.8 | ||
DIAPH2 | ENST00000373049.8 | c.399C>T | p.Thr133Thr | synonymous_variant | Exon 4 of 27 | 1 | ENSP00000362140.4 |
Frequencies
GnomAD3 genomes AF: 0.0000539 AC: 6AN: 111276Hom.: 0 Cov.: 23 AF XY: 0.0000298 AC XY: 1AN XY: 33506
GnomAD3 exomes AF: 0.0000684 AC: 12AN: 175468Hom.: 0 AF XY: 0.0000329 AC XY: 2AN XY: 60702
GnomAD4 exome AF: 0.0000266 AC: 29AN: 1092172Hom.: 0 Cov.: 29 AF XY: 0.0000167 AC XY: 6AN XY: 358442
GnomAD4 genome AF: 0.0000539 AC: 6AN: 111276Hom.: 0 Cov.: 23 AF XY: 0.0000298 AC XY: 1AN XY: 33506
ClinVar
Submissions by phenotype
DIAPH2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at