13-71489023-T-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_080759.6(DACH1):c.1696A>G(p.Ile566Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000434 in 1,613,644 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I566M) has been classified as Uncertain significance.
Frequency
Consequence
NM_080759.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DACH1 | NM_080759.6 | c.1696A>G | p.Ile566Val | missense_variant | 7/11 | ENST00000613252.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DACH1 | ENST00000613252.5 | c.1696A>G | p.Ile566Val | missense_variant | 7/11 | 1 | NM_080759.6 | P2 | |
DACH1 | ENST00000619232.2 | c.1852A>G | p.Ile618Val | missense_variant | 8/12 | 5 | A2 | ||
DACH1 | ENST00000706274.1 | c.1078A>G | p.Ile360Val | missense_variant | 6/10 | ||||
DACH1 | ENST00000706275.1 | c.673A>G | p.Ile225Val | missense_variant | 6/10 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152024Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249104Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135124
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461620Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727124
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152024Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74256
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 25, 2023 | The c.1702A>G (p.I568V) alteration is located in exon 7 (coding exon 7) of the DACH1 gene. This alteration results from a A to G substitution at nucleotide position 1702, causing the isoleucine (I) at amino acid position 568 to be replaced by a valine (V). 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