chr22-46690119-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_022766.6(CERK):c.1414C>T(p.Leu472Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000424 in 1,614,078 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022766.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CERK | NM_022766.6 | c.1414C>T | p.Leu472Phe | missense_variant | 12/13 | ENST00000216264.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CERK | ENST00000216264.13 | c.1414C>T | p.Leu472Phe | missense_variant | 12/13 | 1 | NM_022766.6 | P1 | |
CERK | ENST00000443629.5 | c.*792C>T | 3_prime_UTR_variant, NMD_transcript_variant | 11/12 | 1 | ||||
CERK | ENST00000471929.1 | n.503C>T | non_coding_transcript_exon_variant | 4/4 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.000381 AC: 58AN: 152098Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000529 AC: 133AN: 251436Hom.: 0 AF XY: 0.000537 AC XY: 73AN XY: 135914
GnomAD4 exome AF: 0.000428 AC: 626AN: 1461862Hom.: 2 Cov.: 31 AF XY: 0.000439 AC XY: 319AN XY: 727230
GnomAD4 genome ? AF: 0.000388 AC: 59AN: 152216Hom.: 0 Cov.: 31 AF XY: 0.000403 AC XY: 30AN XY: 74414
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 22, 2022 | The c.1414C>T (p.L472F) alteration is located in exon 12 (coding exon 12) of the CERK gene. This alteration results from a C to T substitution at nucleotide position 1414, causing the leucine (L) at amino acid position 472 to be replaced by a phenylalanine (F). 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