20-3190691-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000354488.8(DDRGK1):c.907G>A(p.Ala303Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 1,613,878 control chromosomes in the GnomAD database, including 23,621 homozygotes. 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 Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
ENST00000354488.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DDRGK1 | NM_023935.3 | c.907G>A | p.Ala303Thr | missense_variant | 9/9 | ENST00000354488.8 | NP_076424.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DDRGK1 | ENST00000354488.8 | c.907G>A | p.Ala303Thr | missense_variant | 9/9 | 1 | NM_023935.3 | ENSP00000346483 | P1 | |
DDRGK1 | ENST00000496781.1 | n.524G>A | non_coding_transcript_exon_variant | 2/2 | 1 | |||||
DDRGK1 | ENST00000470203.1 | n.309G>A | non_coding_transcript_exon_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.127 AC: 19362AN: 152036Hom.: 1664 Cov.: 32
GnomAD3 exomes AF: 0.137 AC: 34330AN: 250710Hom.: 2840 AF XY: 0.140 AC XY: 18985AN XY: 135574
GnomAD4 exome AF: 0.166 AC: 242901AN: 1461724Hom.: 21957 Cov.: 32 AF XY: 0.165 AC XY: 120057AN XY: 727154
GnomAD4 genome AF: 0.127 AC: 19356AN: 152154Hom.: 1664 Cov.: 32 AF XY: 0.126 AC XY: 9369AN XY: 74362
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at