chr4-150079377-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_001040260.4(DCLK2):c.350C>T(p.Pro117Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000126 in 1,588,734 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001040260.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCLK2 | NM_001040260.4 | c.350C>T | p.Pro117Leu | missense_variant | 1/16 | ENST00000296550.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCLK2 | ENST00000296550.12 | c.350C>T | p.Pro117Leu | missense_variant | 1/16 | 1 | NM_001040260.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152014Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000102 AC: 21AN: 205778Hom.: 0 AF XY: 0.0000812 AC XY: 9AN XY: 110826
GnomAD4 exome AF: 0.0000132 AC: 19AN: 1436720Hom.: 0 Cov.: 31 AF XY: 0.0000154 AC XY: 11AN XY: 712374
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152014Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74244
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2022 | The c.350C>T (p.P117L) alteration is located in exon 1 (coding exon 1) of the DCLK2 gene. This alteration results from a C to T substitution at nucleotide position 350, causing the proline (P) at amino acid position 117 to be replaced by a leucine (L). 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