X-154776813-CAAGAAGAAG-CAAGAAG
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_001363.5(DKC1):c.1512_1514delGAA(p.Lys505del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00286 in 1,059,870 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 353 hemizygotes in GnomAD. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001363.5 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000958 AC: 105AN: 109632Hom.: 0 Cov.: 22 AF XY: 0.000990 AC XY: 32AN XY: 32310
GnomAD3 exomes AF: 0.00425 AC: 545AN: 128377Hom.: 0 AF XY: 0.00116 AC XY: 51AN XY: 43799
GnomAD4 exome AF: 0.00308 AC: 2930AN: 950193Hom.: 0 AF XY: 0.00104 AC XY: 321AN XY: 308425
GnomAD4 genome AF: 0.000957 AC: 105AN: 109677Hom.: 0 Cov.: 22 AF XY: 0.000989 AC XY: 32AN XY: 32367
ClinVar
Submissions by phenotype
not specified Uncertain:1Benign:3
- -
- -
- -
- -
not provided Benign:3
- -
- -
- -
Dyskeratosis congenita Benign:3
- -
This alteration is classified as 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. -
- -
DKC1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Dyskeratosis congenita, X-linked Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at