5-77077644-C-G
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_032367.4(ZBED3):āc.235G>Cā(p.Gly79Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000318 in 1,258,684 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 (ā ).
Frequency
Genomes: not found (cov: 32)
Exomes š: 0.0000032 ( 0 hom. )
Consequence
ZBED3
NM_032367.4 missense
NM_032367.4 missense
Scores
4
1
14
Clinical Significance
Conservation
PhyloP100: -0.785
Genes affected
ZBED3 (HGNC:20711): (zinc finger BED-type containing 3) This gene belongs to a class of genes that arose through hAT DNA transposition and that encode regulatory proteins. This gene is upregulated in lung cancer tissues, where the encoded protein causes an accumulation of beta-catenin and enhanced lung cancer cell invasion. In addition, the encoded protein can be secreted and be involved in resistance to insulin. [provided by RefSeq, Jul 2016]
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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=0.301857).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZBED3 | NM_032367.4 | c.235G>C | p.Gly79Arg | missense_variant | 3/3 | ENST00000255198.3 | |
ZBED3 | NM_001329564.2 | c.235G>C | p.Gly79Arg | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZBED3 | ENST00000255198.3 | c.235G>C | p.Gly79Arg | missense_variant | 3/3 | 1 | NM_032367.4 | P1 | |
ZBED3 | ENST00000511587.1 | c.235G>C | p.Gly79Arg | missense_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000318 AC: 4AN: 1258684Hom.: 0 Cov.: 31 AF XY: 0.00000323 AC XY: 2AN XY: 619424
GnomAD4 exome
AF:
AC:
4
AN:
1258684
Hom.:
Cov.:
31
AF XY:
AC XY:
2
AN XY:
619424
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
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 | Nov 18, 2023 | The c.235G>C (p.G79R) alteration is located in exon 3 (coding exon 1) of the ZBED3 gene. This alteration results from a G to C substitution at nucleotide position 235, causing the glycine (G) at amino acid position 79 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
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
M_CAP
Pathogenic
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.
MutationTaster
Benign
N
PrimateAI
Pathogenic
T
PROVEAN
Pathogenic
D;D
REVEL
Benign
Sift
Benign
T;D
Sift4G
Benign
T;.
Polyphen
D;.
Vest4
MutPred
Gain of solvent accessibility (P = 0.0012);Gain of solvent accessibility (P = 0.0012);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at