7-149223955-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003575.4(ZNF282):c.1324C>T(p.Pro442Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000106 in 1,303,840 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
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF282 | NM_003575.4 | c.1324C>T | p.Pro442Ser | missense_variant | 8/8 | ENST00000610704.5 | |
ZNF282 | NM_001303481.3 | c.1324C>T | p.Pro442Ser | missense_variant | 8/9 | ||
ZNF282 | XM_006716151.5 | c.1327C>T | p.Pro443Ser | missense_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF282 | ENST00000610704.5 | c.1324C>T | p.Pro442Ser | missense_variant | 8/8 | 1 | NM_003575.4 | P1 | |
ZNF282 | ENST00000479907.1 | c.1324C>T | p.Pro442Ser | missense_variant | 8/9 | 2 | |||
ZNF282 | ENST00000470381.1 | n.422C>T | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000527 AC: 8AN: 151838Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.000113 AC: 130AN: 1152002Hom.: 0 Cov.: 34 AF XY: 0.000107 AC XY: 59AN XY: 553962
GnomAD4 genome AF: 0.0000527 AC: 8AN: 151838Hom.: 0 Cov.: 32 AF XY: 0.0000674 AC XY: 5AN XY: 74132
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 06, 2023 | The c.1324C>T (p.P442S) alteration is located in exon 8 (coding exon 8) of the ZNF282 gene. This alteration results from a C to T substitution at nucleotide position 1324, causing the proline (P) at amino acid position 442 to be replaced by a serine (S). 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