chr4-150232339-A-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001040260.4(DCLK2):āc.1302A>Gā(p.Glu434=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000229 in 1,613,776 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_001040260.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCLK2 | NM_001040260.4 | c.1302A>G | p.Glu434= | splice_region_variant, synonymous_variant | 9/16 | ENST00000296550.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCLK2 | ENST00000296550.12 | c.1302A>G | p.Glu434= | splice_region_variant, synonymous_variant | 9/16 | 1 | NM_001040260.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 152188Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000251 AC: 63AN: 251020Hom.: 0 AF XY: 0.000221 AC XY: 30AN XY: 135634
GnomAD4 exome AF: 0.000232 AC: 339AN: 1461588Hom.: 0 Cov.: 31 AF XY: 0.000217 AC XY: 158AN XY: 727058
GnomAD4 genome AF: 0.000204 AC: 31AN: 152188Hom.: 0 Cov.: 33 AF XY: 0.000161 AC XY: 12AN XY: 74336
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2023 | DCLK2: BP4, BP7 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at