chr2-200853415-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004071.4(CLK1):c.1346G>A(p.Arg449His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000275 in 1,454,366 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict 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. R449C) has been classified as Likely benign.
Frequency
Consequence
NM_004071.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLK1 | NM_004071.4 | c.1346G>A | p.Arg449His | missense_variant | Exon 13 of 13 | ENST00000321356.9 | NP_004062.2 | |
CLK1 | NM_001162407.1 | c.1472G>A | p.Arg491His | missense_variant | Exon 13 of 13 | NP_001155879.1 | ||
CLK1 | NR_027855.2 | n.1350G>A | non_coding_transcript_exon_variant | Exon 12 of 12 | ||||
CLK1 | NR_027856.2 | n.2841G>A | non_coding_transcript_exon_variant | Exon 11 of 11 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000247 AC: 6AN: 242638Hom.: 0 AF XY: 0.0000153 AC XY: 2AN XY: 130938
GnomAD4 exome AF: 0.0000275 AC: 40AN: 1454366Hom.: 0 Cov.: 30 AF XY: 0.0000304 AC XY: 22AN XY: 723158
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1472G>A (p.R491H) alteration is located in exon 13 (coding exon 13) of the CLK1 gene. This alteration results from a G to A substitution at nucleotide position 1472, causing the arginine (R) at amino acid position 491 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