5-177504350-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001308236.3(DOK3):āc.956A>Cā(p.Asp319Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000633 in 1,580,038 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D319Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_001308236.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DOK3 | NM_001308236.3 | c.956A>C | p.Asp319Ala | missense_variant | 6/6 | ENST00000510898.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOK3 | ENST00000510898.7 | c.956A>C | p.Asp319Ala | missense_variant | 6/6 | 3 | NM_001308236.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152178Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000269 AC: 6AN: 222716Hom.: 0 AF XY: 0.0000333 AC XY: 4AN XY: 120298
GnomAD4 exome AF: 0.00000630 AC: 9AN: 1427860Hom.: 0 Cov.: 30 AF XY: 0.00000708 AC XY: 5AN XY: 705736
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152178Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 10, 2022 | The c.1124A>C (p.D375A) alteration is located in exon 6 (coding exon 6) of the DOK3 gene. This alteration results from a A to C substitution at nucleotide position 1124, causing the aspartic acid (D) at amino acid position 375 to be replaced by an alanine (A). 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