7-149212432-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.1027G>A(p.Asp343Asn) variant causes a missense change. The variant allele was found at a frequency of 0.000189 in 1,613,178 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 0.00016 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00019 ( 0 hom. )
Consequence
ZNF282
NM_003575.4 missense
NM_003575.4 missense
Scores
1
5
10
Clinical Significance
Conservation
PhyloP100: 4.06
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=0.15484977).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF282 | NM_003575.4 | c.1027G>A | p.Asp343Asn | missense_variant | 6/8 | ENST00000610704.5 | |
ZNF282 | NM_001303481.3 | c.1027G>A | p.Asp343Asn | missense_variant | 6/9 | ||
ZNF282 | XM_006716151.5 | c.1030G>A | p.Asp344Asn | missense_variant | 6/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF282 | ENST00000610704.5 | c.1027G>A | p.Asp343Asn | missense_variant | 6/8 | 1 | NM_003575.4 | P1 | |
ZNF282 | ENST00000479907.1 | c.1027G>A | p.Asp343Asn | missense_variant | 6/9 | 2 | |||
ZNF282 | ENST00000470381.1 | n.125G>A | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152198Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000156 AC: 39AN: 249744Hom.: 0 AF XY: 0.000178 AC XY: 24AN XY: 134992
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GnomAD4 exome AF: 0.000192 AC: 281AN: 1460862Hom.: 0 Cov.: 30 AF XY: 0.000182 AC XY: 132AN XY: 726686
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GnomAD4 genome AF: 0.000158 AC: 24AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74486
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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 | May 14, 2024 | The c.1027G>A (p.D343N) alteration is located in exon 6 (coding exon 6) of the ZNF282 gene. This alteration results from a G to A substitution at nucleotide position 1027, causing the aspartic acid (D) at amino acid position 343 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Pathogenic
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
Uncertain
M;M
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
Sift4G
Benign
T;T
Polyphen
D;.
Vest4
MVP
ClinPred
T
GERP RS
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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