chr5-177503139-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The ENST00000312943.10(DOK3):c.899A>G(p.Gln300Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00146 in 1,549,548 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000312943.10 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DOK3 | NM_001308236.3 | c.*844A>G | 3_prime_UTR_variant | 6/6 | ENST00000510898.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOK3 | ENST00000510898.7 | c.*844A>G | 3_prime_UTR_variant | 6/6 | 3 | NM_001308236.3 | P1 | ||
PDLIM7-AS1 | ENST00000506025.1 | n.145-219T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00127 AC: 191AN: 150092Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00109 AC: 165AN: 151368Hom.: 0 AF XY: 0.00102 AC XY: 82AN XY: 80524
GnomAD4 exome AF: 0.00148 AC: 2071AN: 1399338Hom.: 2 Cov.: 87 AF XY: 0.00150 AC XY: 1037AN XY: 690186
GnomAD4 genome ? AF: 0.00127 AC: 191AN: 150210Hom.: 0 Cov.: 33 AF XY: 0.00131 AC XY: 96AN XY: 73282
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 13, 2021 | The c.899A>G (p.Q300R) alteration is located in exon 6 (coding exon 5) of the DOK3 gene. This alteration results from a A to G substitution at nucleotide position 899, causing the glutamine (Q) at amino acid position 300 to be replaced by an arginine (R). 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