chr7-149223899-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_003575.4(ZNF282):c.1268C>T(p.Ser423Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000666 in 1,410,854 control chromosomes in the GnomAD database, including 2 homozygotes. 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF282 | NM_003575.4 | c.1268C>T | p.Ser423Leu | missense_variant | 8/8 | ENST00000610704.5 | |
ZNF282 | NM_001303481.3 | c.1268C>T | p.Ser423Leu | missense_variant | 8/9 | ||
ZNF282 | XM_006716151.5 | c.1271C>T | p.Ser424Leu | missense_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF282 | ENST00000610704.5 | c.1268C>T | p.Ser423Leu | missense_variant | 8/8 | 1 | NM_003575.4 | P1 | |
ZNF282 | ENST00000479907.1 | c.1268C>T | p.Ser423Leu | missense_variant | 8/9 | 2 | |||
ZNF282 | ENST00000470381.1 | n.366C>T | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 151912Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000106 AC: 4AN: 37744Hom.: 1 AF XY: 0.000183 AC XY: 4AN XY: 21826
GnomAD4 exome AF: 0.0000572 AC: 72AN: 1258942Hom.: 2 Cov.: 34 AF XY: 0.0000600 AC XY: 37AN XY: 616858
GnomAD4 genome AF: 0.000145 AC: 22AN: 151912Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74178
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.1268C>T (p.S423L) 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 1268, causing the serine (S) at amino acid position 423 to be replaced by a leucine (L). 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