20-3190681-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_023935.3(DDRGK1):c.917G>A(p.Arg306Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000508 in 1,613,766 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_023935.3 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 |
---|---|---|---|---|---|---|---|
DDRGK1 | NM_023935.3 | c.917G>A | p.Arg306Gln | missense_variant | 9/9 | ENST00000354488.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DDRGK1 | ENST00000354488.8 | c.917G>A | p.Arg306Gln | missense_variant | 9/9 | 1 | NM_023935.3 | P1 | |
DDRGK1 | ENST00000496781.1 | n.534G>A | non_coding_transcript_exon_variant | 2/2 | 1 | ||||
DDRGK1 | ENST00000470203.1 | n.319G>A | non_coding_transcript_exon_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000878 AC: 22AN: 250534Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135500
GnomAD4 exome AF: 0.0000513 AC: 75AN: 1461604Hom.: 0 Cov.: 30 AF XY: 0.0000646 AC XY: 47AN XY: 727118
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74318
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 17, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at