chr22-46690151-G-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_022766.6(CERK):c.1382C>T(p.Thr461Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000726 in 1,613,972 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0040 ( 4 hom., cov: 31)
Exomes 𝑓: 0.00038 ( 2 hom. )
Consequence
CERK
NM_022766.6 missense
NM_022766.6 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: 1.18
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 -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.010273844).
BP6
Variant 22-46690151-G-A is Benign according to our data. Variant chr22-46690151-G-A is described in ClinVar as [Benign]. Clinvar id is 731194.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CERK | NM_022766.6 | c.1382C>T | p.Thr461Met | missense_variant | 12/13 | ENST00000216264.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CERK | ENST00000216264.13 | c.1382C>T | p.Thr461Met | missense_variant | 12/13 | 1 | NM_022766.6 | P1 | |
CERK | ENST00000443629.5 | c.*760C>T | 3_prime_UTR_variant, NMD_transcript_variant | 11/12 | 1 | ||||
CERK | ENST00000471929.1 | n.471C>T | non_coding_transcript_exon_variant | 4/4 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00405 AC: 616AN: 152002Hom.: 4 Cov.: 31
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GnomAD3 exomes AF: 0.00103 AC: 259AN: 251470Hom.: 1 AF XY: 0.000714 AC XY: 97AN XY: 135914
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GnomAD4 exome AF: 0.000380 AC: 555AN: 1461852Hom.: 2 Cov.: 31 AF XY: 0.000329 AC XY: 239AN XY: 727218
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GnomAD4 genome AF: 0.00405 AC: 616AN: 152120Hom.: 4 Cov.: 31 AF XY: 0.00383 AC XY: 285AN XY: 74362
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 21, 2018 | - - |
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
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
N;N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
P
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