chrX-86812933-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_053281.3(DACH2):c.1318G>A(p.Ala440Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000589 in 1,205,172 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 20 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_053281.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DACH2 | NM_053281.3 | c.1318G>A | p.Ala440Thr | missense_variant | 8/12 | ENST00000373125.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DACH2 | ENST00000373125.9 | c.1318G>A | p.Ala440Thr | missense_variant | 8/12 | 1 | NM_053281.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000135 AC: 15AN: 111477Hom.: 0 Cov.: 22 AF XY: 0.0000891 AC XY: 3AN XY: 33653
GnomAD3 exomes AF: 0.0000445 AC: 8AN: 179964Hom.: 0 AF XY: 0.0000464 AC XY: 3AN XY: 64596
GnomAD4 exome AF: 0.0000512 AC: 56AN: 1093695Hom.: 0 Cov.: 29 AF XY: 0.0000473 AC XY: 17AN XY: 359251
GnomAD4 genome ? AF: 0.000135 AC: 15AN: 111477Hom.: 0 Cov.: 22 AF XY: 0.0000891 AC XY: 3AN XY: 33653
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 14, 2023 | The c.1318G>A (p.A440T) alteration is located in exon 8 (coding exon 8) of the DACH2 gene. This alteration results from a G to A substitution at nucleotide position 1318, causing the alanine (A) at amino acid position 440 to be replaced by a threonine (T). 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