17-56834816-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_003647.3(DGKE):c.21G>C(p.Pro7=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000489 in 1,451,946 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P7P) has been classified as Likely benign.
Frequency
Consequence
NM_003647.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DGKE | NM_003647.3 | c.21G>C | p.Pro7= | synonymous_variant | 2/12 | ENST00000284061.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DGKE | ENST00000284061.8 | c.21G>C | p.Pro7= | synonymous_variant | 2/12 | 1 | NM_003647.3 | P1 | |
DGKE | ENST00000572810.1 | c.21G>C | p.Pro7= | synonymous_variant | 2/2 | 1 | |||
DGKE | ENST00000576869.5 | n.169G>C | non_coding_transcript_exon_variant | 2/6 | 1 | ||||
C17orf67 | ENST00000487705.1 | n.285+3673C>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000459 AC: 11AN: 239748Hom.: 0 AF XY: 0.0000458 AC XY: 6AN XY: 131088
GnomAD4 exome AF: 0.0000489 AC: 71AN: 1451946Hom.: 0 Cov.: 31 AF XY: 0.0000416 AC XY: 30AN XY: 721464
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at