chr12-112941739-T-C
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006187.4(OAS3):āc.347T>Cā(p.Leu116Pro) variant causes a missense change. The variant allele was found at a frequency of 0.0000219 in 1,461,712 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes š: 0.000022 ( 0 hom. )
Consequence
OAS3
NM_006187.4 missense
NM_006187.4 missense
Scores
2
5
12
Clinical Significance
Conservation
PhyloP100: 4.28
Genes affected
OAS3 (HGNC:8088): (2'-5'-oligoadenylate synthetase 3) This gene encodes an enzyme included in the 2', 5' oligoadenylate synthase family. This enzyme is induced by interferons and catalyzes the 2', 5' oligomers of adenosine in order to bind and activate RNase L. This enzyme family plays a significant role in the inhibition of cellular protein synthesis and viral infection resistance. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OAS3 | NM_006187.4 | c.347T>C | p.Leu116Pro | missense_variant | 2/16 | ENST00000228928.12 | NP_006178.2 | |
OAS3 | NM_001410984.1 | c.347T>C | p.Leu116Pro | missense_variant | 2/16 | NP_001397913.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OAS3 | ENST00000228928.12 | c.347T>C | p.Leu116Pro | missense_variant | 2/16 | 1 | NM_006187.4 | ENSP00000228928.7 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.000112 AC: 28AN: 249242Hom.: 0 AF XY: 0.0000888 AC XY: 12AN XY: 135210
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GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461712Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 727138
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GnomAD4 genome Cov.: 32
GnomAD4 genome
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32
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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 | Oct 20, 2024 | The c.347T>C (p.L116P) alteration is located in exon 2 (coding exon 2) of the OAS3 gene. This alteration results from a T to C substitution at nucleotide position 347, causing the leucine (L) at amino acid position 116 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.;T
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;T;T
M_CAP
Benign
T
MetaRNN
Uncertain
D;D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.;.
PrimateAI
Benign
T
PROVEAN
Benign
N;D;D
REVEL
Benign
Sift
Uncertain
D;D;D
Sift4G
Pathogenic
D;D;D
Polyphen
D;D;D
Vest4
MutPred
Gain of catalytic residue at P112 (P = 4e-04);Gain of catalytic residue at P112 (P = 4e-04);Gain of catalytic residue at P112 (P = 4e-04);
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