rs770650860
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4BP6
The NM_001024736.2(CD276):c.338G>A(p.Arg113His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000347 in 1,612,878 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000036 ( 1 hom. )
Consequence
CD276
NM_001024736.2 missense
NM_001024736.2 missense
Scores
1
5
10
Clinical Significance
Conservation
PhyloP100: 1.23
Genes affected
CD276 (HGNC:19137): (CD276 molecule) The protein encoded by this gene belongs to the immunoglobulin superfamily, and thought to participate in the regulation of T-cell-mediated immune response. Studies show that while the transcript of this gene is ubiquitously expressed in normal tissues and solid tumors, the protein is preferentially expressed only in tumor tissues. Additionally, it was observed that the 3' UTR of this transcript contains a target site for miR29 microRNA, and there is an inverse correlation between the expression of this protein and miR29 levels, suggesting regulation of expression of this gene product by miR29. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.3907076).
BP6
?
Variant 15-73702513-G-A is Benign according to our data. Variant chr15-73702513-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 207869.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD276 | NM_001024736.2 | c.338G>A | p.Arg113His | missense_variant | 3/10 | ENST00000318443.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD276 | ENST00000318443.10 | c.338G>A | p.Arg113His | missense_variant | 3/10 | 2 | NM_001024736.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152206Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000282 AC: 7AN: 248224Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134674
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GnomAD4 exome AF: 0.0000356 AC: 52AN: 1460672Hom.: 1 Cov.: 34 AF XY: 0.0000427 AC XY: 31AN XY: 726744
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GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74346
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Long QT syndrome Benign:1
Likely benign, no assertion criteria provided | research | Medical Research Institute, Tokyo Medical and Dental University | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Benign
T;T;.;T;.;.;T;T;.
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Benign
N
M_CAP
Uncertain
D
MetaRNN
Benign
T;T;T;T;T;T;T;T;T
MetaSVM
Uncertain
T
MutationTaster
Benign
D;D;D;N;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N;N;N;D;N
Sift
Uncertain
D;D;D;D;D;D;D;D;D
Sift4G
Benign
T;D;T;T;T;D;T;T;T
Polyphen
0.99, 1.0, 0.98
.;D;D;.;.;D;.;.;D
Vest4
0.097, 0.11, 0.10
MutPred
Gain of catalytic residue at R111 (P = 0.0763);Gain of catalytic residue at R111 (P = 0.0763);Gain of catalytic residue at R111 (P = 0.0763);Gain of catalytic residue at R111 (P = 0.0763);Gain of catalytic residue at R111 (P = 0.0763);Gain of catalytic residue at R111 (P = 0.0763);Gain of catalytic residue at R111 (P = 0.0763);Gain of catalytic residue at R111 (P = 0.0763);Gain of catalytic residue at R111 (P = 0.0763);
MVP
MPC
0.44
ClinPred
T
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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