7-149207437-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003575.4(ZNF282):c.799G>A(p.Glu267Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000281 in 1,564,034 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 Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000030 ( 1 hom. )
Consequence
ZNF282
NM_003575.4 missense
NM_003575.4 missense
Scores
5
11
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.78
Genes affected
ZNF282 (HGNC:13076): (zinc finger protein 282) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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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=0.15781146).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF282 | NM_003575.4 | c.799G>A | p.Glu267Lys | missense_variant | 4/8 | ENST00000610704.5 | |
ZNF282 | NM_001303481.3 | c.799G>A | p.Glu267Lys | missense_variant | 4/9 | ||
ZNF282 | XM_006716151.5 | c.799G>A | p.Glu267Lys | missense_variant | 4/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF282 | ENST00000610704.5 | c.799G>A | p.Glu267Lys | missense_variant | 4/8 | 1 | NM_003575.4 | P1 | |
ZNF282 | ENST00000479907.1 | c.799G>A | p.Glu267Lys | missense_variant | 4/9 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152204Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000465 AC: 8AN: 171902Hom.: 0 AF XY: 0.0000549 AC XY: 5AN XY: 91008
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GnomAD4 exome AF: 0.0000298 AC: 42AN: 1411712Hom.: 1 Cov.: 31 AF XY: 0.0000272 AC XY: 19AN XY: 697528
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152322Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74502
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N
MutationTaster
Benign
N;N
PrimateAI
Uncertain
T
Sift4G
Benign
T;T
Polyphen
D;.
Vest4
MutPred
Gain of ubiquitination at E267 (P = 0.0042);Gain of ubiquitination at E267 (P = 0.0042);
MVP
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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