chr19-464062-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_182577.3(ODF3L2):c.652C>T(p.Arg218Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000456 in 1,580,472 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000059 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000044 ( 0 hom. )
Consequence
ODF3L2
NM_182577.3 missense
NM_182577.3 missense
Scores
5
7
7
Clinical Significance
Conservation
PhyloP100: 2.55
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.41990092).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ODF3L2 | NM_182577.3 | c.652C>T | p.Arg218Cys | missense_variant | 4/4 | ENST00000315489.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CIMAP1D | ENST00000315489.5 | c.652C>T | p.Arg218Cys | missense_variant | 4/4 | 1 | NM_182577.3 | P2 | |
CIMAP1D | ENST00000382696.7 | c.544C>T | p.Arg182Cys | missense_variant | 3/3 | 1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000594 AC: 9AN: 151632Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000859 AC: 16AN: 186280Hom.: 0 AF XY: 0.0000985 AC XY: 10AN XY: 101524
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GnomAD4 exome AF: 0.0000441 AC: 63AN: 1428722Hom.: 0 Cov.: 40 AF XY: 0.0000494 AC XY: 35AN XY: 708134
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GnomAD4 genome AF: 0.0000593 AC: 9AN: 151750Hom.: 0 Cov.: 31 AF XY: 0.0000674 AC XY: 5AN XY: 74166
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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 | May 17, 2023 | The c.652C>T (p.R218C) alteration is located in exon 4 (coding exon 4) of the ODF3L2 gene. This alteration results from a C to T substitution at nucleotide position 652, causing the arginine (R) at amino acid position 218 to be replaced by a cysteine (C). 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
Pathogenic
DANN
Pathogenic
DEOGEN2
Benign
.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Pathogenic
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
.;M
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D
REVEL
Uncertain
Sift
Pathogenic
D;D
Sift4G
Pathogenic
D;D
Polyphen
D;D
Vest4
MVP
MPC
1.0
ClinPred
D
GERP RS
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