22-46690119-G-A
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
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
Genomes: 𝑓 0.00039 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00043 ( 2 hom. )
Consequence
CERK
NM_022766.6 missense
NM_022766.6 missense
Scores
1
18
Clinical Significance
Conservation
PhyloP100: 0.0980
Genes affected
CERK (HGNC:19256): (ceramide kinase) CERK converts ceramide to ceramide 1-phosphate (C1P), a sphingolipid metabolite. Both CERK and C1P have been implicated in various cellular processes, including proliferation, apoptosis, phagocytosis, and inflammation (Kim et al., 2006 [PubMed 16488390]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.007738918).
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CERK | NM_022766.6 | c.1414C>T | p.Leu472Phe | missense_variant | 12/13 | ENST00000216264.13 | NP_073603.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CERK | ENST00000216264.13 | c.1414C>T | p.Leu472Phe | missense_variant | 12/13 | 1 | NM_022766.6 | ENSP00000216264.8 | ||
CERK | ENST00000443629.5 | n.*792C>T | non_coding_transcript_exon_variant | 11/12 | 1 | ENSP00000400859.1 | ||||
CERK | ENST00000443629.5 | n.*792C>T | 3_prime_UTR_variant | 11/12 | 1 | ENSP00000400859.1 | ||||
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
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GnomAD3 exomes AF: 0.000529 AC: 133AN: 251436Hom.: 0 AF XY: 0.000537 AC XY: 73AN XY: 135914
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GnomAD4 exome AF: 0.000428 AC: 626AN: 1461862Hom.: 2 Cov.: 31 AF XY: 0.000439 AC XY: 319AN XY: 727230
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GnomAD4 genome AF: 0.000388 AC: 59AN: 152216Hom.: 0 Cov.: 31 AF XY: 0.000403 AC XY: 30AN XY: 74414
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
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:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at