chr4-150198083-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_001040260.4(DCLK2):c.941G>A(p.Arg314His) variant causes a missense change. The variant allele was found at a frequency of 0.0000105 in 1,613,342 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R314S) has been classified 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 -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCLK2 | NM_001040260.4 | c.941G>A | p.Arg314His | missense_variant | 4/16 | ENST00000296550.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCLK2 | ENST00000296550.12 | c.941G>A | p.Arg314His | missense_variant | 4/16 | 1 | NM_001040260.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152086Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250300Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135268
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461256Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 8AN XY: 726892
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152086Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 23, 2023 | The c.941G>A (p.R314H) alteration is located in exon 4 (coding exon 4) of the DCLK2 gene. This alteration results from a G to A substitution at nucleotide position 941, causing the arginine (R) at amino acid position 314 to be replaced by a histidine (H). 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