chrX-96738667-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_006729.5(DIAPH2):c.247G>A(p.Ala83Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00841 in 1,205,238 control chromosomes in the GnomAD database, including 45 homozygotes. There are 3,158 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A83A) has been classified as Likely benign.
Frequency
Consequence
NM_006729.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DIAPH2 | NM_006729.5 | c.247G>A | p.Ala83Thr | missense_variant | 3/27 | ENST00000324765.13 | |
DIAPH2 | NM_007309.4 | c.247G>A | p.Ala83Thr | missense_variant | 3/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DIAPH2 | ENST00000324765.13 | c.247G>A | p.Ala83Thr | missense_variant | 3/27 | 1 | NM_006729.5 | A2 | |
DIAPH2 | ENST00000373049.8 | c.247G>A | p.Ala83Thr | missense_variant | 3/27 | 1 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00634 AC: 705AN: 111135Hom.: 4 Cov.: 22 AF XY: 0.00512 AC XY: 171AN XY: 33395
GnomAD3 exomes AF: 0.00623 AC: 1125AN: 180556Hom.: 4 AF XY: 0.00577 AC XY: 376AN XY: 65186
GnomAD4 exome AF: 0.00862 AC: 9435AN: 1094054Hom.: 41 Cov.: 28 AF XY: 0.00830 AC XY: 2987AN XY: 359730
GnomAD4 genome ? AF: 0.00634 AC: 705AN: 111184Hom.: 4 Cov.: 22 AF XY: 0.00511 AC XY: 171AN XY: 33454
ClinVar
Submissions by phenotype
Premature ovarian failure 2A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Institute of Human Genetics, University of Leipzig Medical Center | Jan 01, 2019 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at