rs1242996115
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001363.5(DKC1):c.16+5G>A variant causes a splice donor 5th base, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000509 in 1,179,920 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001363.5 splice_donor_5th_base, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DKC1 | NM_001363.5 | c.16+5G>A | splice_donor_5th_base_variant, intron_variant | ENST00000369550.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DKC1 | ENST00000369550.10 | c.16+5G>A | splice_donor_5th_base_variant, intron_variant | 1 | NM_001363.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000889 AC: 1AN: 112500Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34640
GnomAD3 exomes AF: 0.0000154 AC: 2AN: 130109Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 41827
GnomAD4 exome AF: 0.00000468 AC: 5AN: 1067420Hom.: 0 Cov.: 30 AF XY: 0.00000576 AC XY: 2AN XY: 347430
GnomAD4 genome ? AF: 0.00000889 AC: 1AN: 112500Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34640
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Sep 27, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at