chr12-107319088-A-G
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001018072.2(ABTB3):āc.148A>Gā(p.Ser50Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Genomes: not found (cov: 33)
Exomes š: 0.0000034 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ABTB3
NM_001018072.2 missense
NM_001018072.2 missense
Scores
1
18
Clinical Significance
Conservation
PhyloP100: 2.61
Genes affected
ABTB3 (HGNC:23844): (ankyrin repeat and BTB domain containing 3) Predicted to enable protein heterodimerization activity. Predicted to be involved in SMAD protein signal transduction. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.044717103).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABTB3 | NM_001018072.2 | c.148A>G | p.Ser50Gly | missense_variant | 1/17 | ENST00000280758.10 | |
ABTB3 | NM_001347943.2 | c.148A>G | p.Ser50Gly | missense_variant | 1/15 | ||
ABTB3 | XM_047428301.1 | c.148A>G | p.Ser50Gly | missense_variant | 1/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABTB3 | ENST00000280758.10 | c.148A>G | p.Ser50Gly | missense_variant | 1/17 | 5 | NM_001018072.2 | ||
ABTB3 | ENST00000490090.6 | c.148A>G | p.Ser50Gly | missense_variant | 1/15 | 2 | |||
ABTB3 | ENST00000420571.6 | c.148A>G | p.Ser50Gly | missense_variant | 1/15 | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD3 exomes AF: 0.0000253 AC: 6AN: 236732Hom.: 0 AF XY: 0.0000232 AC XY: 3AN XY: 129060
GnomAD3 exomes
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000344 AC: 5AN: 1455558Hom.: 0 Cov.: 31 AF XY: 0.00000553 AC XY: 4AN XY: 723918
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
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1455558
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GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ExAC
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10
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Malignant tumor of prostate Uncertain:1
Uncertain significance, no assertion criteria provided | research | Prostate Cancer Research Center, Institute of Biosciences and Medical Technology, University of Tampere | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Benign
DEOGEN2
Benign
T;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;N
MutationTaster
Benign
N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
B;B;B
Vest4
MutPred
Gain of catalytic residue at C51 (P = 0);Gain of catalytic residue at C51 (P = 0);Gain of catalytic residue at C51 (P = 0);
MVP
MPC
ClinPred
T
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