X-154776813-CAAGAAGAAG-CAAGAAGAAGAAG
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_001363.5(DKC1):c.1512_1514dupGAA(p.Lys505dup) variant causes a disruptive inframe insertion change. The variant allele was found at a frequency of 0.0043 in 1,194,697 control chromosomes in the GnomAD database, including 18 homozygotes. There are 891 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001363.5 disruptive_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00446 AC: 490AN: 109780Hom.: 7 Cov.: 22 AF XY: 0.00395 AC XY: 128AN XY: 32382
GnomAD3 exomes AF: 0.00777 AC: 997AN: 128377Hom.: 3 AF XY: 0.00386 AC XY: 169AN XY: 43799
GnomAD4 exome AF: 0.00428 AC: 4646AN: 1084870Hom.: 12 Cov.: 28 AF XY: 0.00214 AC XY: 761AN XY: 355106
GnomAD4 genome AF: 0.00449 AC: 493AN: 109827Hom.: 6 Cov.: 22 AF XY: 0.00401 AC XY: 130AN XY: 32439
ClinVar
Submissions by phenotype
not provided Benign:4
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Dyskeratosis congenita, X-linked Benign:3
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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. -
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not specified Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at