chr22-40156152-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The ENST00000402203.5(TNRC6B):c.83A>G(p.Lys28Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000657 in 152,240 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 0.0000066 ( 0 hom., cov: 32)
Consequence
TNRC6B
ENST00000402203.5 missense
ENST00000402203.5 missense
Scores
3
3
9
Clinical Significance
Conservation
PhyloP100: 5.72
Genes affected
TNRC6B (HGNC:29190): (trinucleotide repeat containing adaptor 6B) Enables RNA binding activity. Involved in regulation of gene expression. Predicted to be located in cytosol. Predicted to be active in P-body and nucleoplasm. Implicated in subserous uterine fibroid and uterine fibroid. [provided by Alliance of Genome Resources, Apr 2022]
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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=0.3043748).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNRC6B | NM_001024843.2 | c.83A>G | p.Lys28Arg | missense_variant | 4/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNRC6B | ENST00000402203.5 | c.83A>G | p.Lys28Arg | missense_variant | 4/24 | 1 | A2 | ||
TNRC6B | ENST00000301923.13 | c.83A>G | p.Lys28Arg | missense_variant | 4/24 | 5 | A2 | ||
TNRC6B | ENST00000441751.5 | c.83A>G | p.Lys28Arg | missense_variant | 4/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152240Hom.: 0 Cov.: 32
GnomAD3 genomes
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GnomAD4 exome Cov.: 30
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30
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74378
GnomAD4 genome
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 29, 2022 | The c.83A>G (p.K28R) alteration is located in exon 4 (coding exon 2) of the TNRC6B gene. This alteration results from a A to G substitution at nucleotide position 83, causing the lysine (K) at amino acid position 28 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Pathogenic
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;.
M_CAP
Benign
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N
PROVEAN
Uncertain
D;N;N
REVEL
Benign
Sift
Pathogenic
D;T;T
Sift4G
Pathogenic
D;T;T
Polyphen
0.97
.;D;D
Vest4
0.40, 0.39
MutPred
Loss of ubiquitination at K28 (P = 0.002);Loss of ubiquitination at K28 (P = 0.002);Loss of ubiquitination at K28 (P = 0.002);
MVP
ClinPred
D
GERP RS
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at