chr7-149198624-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003575.4(ZNF282):c.457G>A(p.Val153Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000508 in 1,614,048 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003575.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF282 | NM_003575.4 | c.457G>A | p.Val153Met | missense_variant | 2/8 | ENST00000610704.5 | |
ZNF282 | NM_001303481.3 | c.457G>A | p.Val153Met | missense_variant | 2/9 | ||
ZNF282 | XM_006716151.5 | c.457G>A | p.Val153Met | missense_variant | 2/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF282 | ENST00000610704.5 | c.457G>A | p.Val153Met | missense_variant | 2/8 | 1 | NM_003575.4 | P1 | |
ZNF282 | ENST00000479907.1 | c.457G>A | p.Val153Met | missense_variant | 2/9 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251318Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135896
GnomAD4 exome AF: 0.0000493 AC: 72AN: 1461858Hom.: 0 Cov.: 31 AF XY: 0.0000564 AC XY: 41AN XY: 727230
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 01, 2024 | The c.457G>A (p.V153M) alteration is located in exon 2 (coding exon 2) of the ZNF282 gene. This alteration results from a G to A substitution at nucleotide position 457, causing the valine (V) at amino acid position 153 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at