rs374771308
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4BP6BS2
The NM_001363.5(DKC1):c.622G>A(p.Asp208Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000587 in 1,210,012 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 26 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001363.5 missense
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 |
---|---|---|---|---|---|---|---|
DKC1 | NM_001363.5 | c.622G>A | p.Asp208Asn | missense_variant | 7/15 | ENST00000369550.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DKC1 | ENST00000369550.10 | c.622G>A | p.Asp208Asn | missense_variant | 7/15 | 1 | NM_001363.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 14AN: 112011Hom.: 0 Cov.: 23 AF XY: 0.000146 AC XY: 5AN XY: 34205
GnomAD3 exomes AF: 0.0000163 AC: 3AN: 183518Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67948
GnomAD4 exome AF: 0.0000519 AC: 57AN: 1098001Hom.: 0 Cov.: 31 AF XY: 0.0000578 AC XY: 21AN XY: 363359
GnomAD4 genome ? AF: 0.000125 AC: 14AN: 112011Hom.: 0 Cov.: 23 AF XY: 0.000146 AC XY: 5AN XY: 34205
ClinVar
Submissions by phenotype
Dyskeratosis congenita Uncertain:1Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 08, 2022 | The c.622G>A (p.D208N) alteration is located in exon 7 (coding exon 7) of the DKC1 gene. This alteration results from a G to A substitution at nucleotide position 622, causing the aspartic acid (D) at amino acid position 208 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at