chrX-86714701-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_053281.3(DACH2):c.1085C>G(p.Ala362Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000059 in 1,170,228 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 22 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 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
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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.1085C>G | p.Ala362Gly | missense_variant | 6/12 | ENST00000373125.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DACH2 | ENST00000373125.9 | c.1085C>G | p.Ala362Gly | missense_variant | 6/12 | 1 | NM_053281.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000536 AC: 6AN: 112044Hom.: 0 Cov.: 23 AF XY: 0.0000877 AC XY: 3AN XY: 34214
GnomAD3 exomes AF: 0.0000294 AC: 5AN: 169954Hom.: 0 AF XY: 0.0000178 AC XY: 1AN XY: 56092
GnomAD4 exome AF: 0.0000595 AC: 63AN: 1058184Hom.: 0 Cov.: 29 AF XY: 0.0000571 AC XY: 19AN XY: 332476
GnomAD4 genome ? AF: 0.0000536 AC: 6AN: 112044Hom.: 0 Cov.: 23 AF XY: 0.0000877 AC XY: 3AN XY: 34214
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2022 | The c.1085C>G (p.A362G) alteration is located in exon 6 (coding exon 6) of the DACH2 gene. This alteration results from a C to G substitution at nucleotide position 1085, causing the alanine (A) at amino acid position 362 to be replaced by a glycine (G). 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